library(dplyr)##
## Attaching package: 'dplyr'## The following objects are masked from 'package:stats':
##
## filter, lag## The following objects are masked from 'package:base':
##
## intersect, setdiff, setequal, union# Set your working directory to the directory where the data was downloaded
# or any other suitable folder with the data
setwd("C:/Users/ghosh/Downloads")
# Downloaded data. CHANGE THE FILE NAME ACCORDINGLY
tar_gz_file = "gdc_download_20240109_134313.650403.tar.gz"
# Uncompress the downloaded data in
untar(tar_gz_file, exdir = "gdc_data")
# Read mutation data in a data frame
mut_data = read.table(list.files(path = "gdc_data", pattern = ".gz$",full.names = T, recursive = T)[1],
header = TRUE, comment.char = "#", sep = "\t")## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
## : EOF within quoted string## Warning in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,
## : number of items read is not a multiple of the number of columns# Explore the column headers
colnames(mut_data)## [1] "Hugo_Symbol" "Entrez_Gene_Id"
## [3] "Center" "NCBI_Build"
## [5] "Chromosome" "Start_Position"
## [7] "End_Position" "Strand"
## [9] "Variant_Classification" "Variant_Type"
## [11] "Reference_Allele" "Tumor_Seq_Allele1"
## [13] "Tumor_Seq_Allele2" "dbSNP_RS"
## [15] "dbSNP_Val_Status" "Tumor_Sample_Barcode"
## [17] "Matched_Norm_Sample_Barcode" "Match_Norm_Seq_Allele1"
## [19] "Match_Norm_Seq_Allele2" "Tumor_Validation_Allele1"
## [21] "Tumor_Validation_Allele2" "Match_Norm_Validation_Allele1"
## [23] "Match_Norm_Validation_Allele2" "Verification_Status"
## [25] "Validation_Status" "Mutation_Status"
## [27] "Sequencing_Phase" "Sequence_Source"
## [29] "Validation_Method" "Score"
## [31] "BAM_File" "Sequencer"
## [33] "Tumor_Sample_UUID" "Matched_Norm_Sample_UUID"
## [35] "HGVSc" "HGVSp"
## [37] "HGVSp_Short" "Transcript_ID"
## [39] "Exon_Number" "t_depth"
## [41] "t_ref_count" "t_alt_count"
## [43] "n_depth" "n_ref_count"
## [45] "n_alt_count" "all_effects"
## [47] "Allele" "Gene"
## [49] "Feature" "Feature_type"
## [51] "One_Consequence" "Consequence"
## [53] "cDNA_position" "CDS_position"
## [55] "Protein_position" "Amino_acids"
## [57] "Codons" "Existing_variation"
## [59] "DISTANCE" "TRANSCRIPT_STRAND"
## [61] "SYMBOL" "SYMBOL_SOURCE"
## [63] "HGNC_ID" "BIOTYPE"
## [65] "CANONICAL" "CCDS"
## [67] "ENSP" "SWISSPROT"
## [69] "TREMBL" "UNIPARC"
## [71] "UNIPROT_ISOFORM" "RefSeq"
## [73] "MANE" "APPRIS"
## [75] "FLAGS" "SIFT"
## [77] "PolyPhen" "EXON"
## [79] "INTRON" "DOMAINS"
## [81] "X1000G_AF" "X1000G_AFR_AF"
## [83] "X1000G_AMR_AF" "X1000G_EAS_AF"
## [85] "X1000G_EUR_AF" "X1000G_SAS_AF"
## [87] "ESP_AA_AF" "ESP_EA_AF"
## [89] "gnomAD_AF" "gnomAD_AFR_AF"
## [91] "gnomAD_AMR_AF" "gnomAD_ASJ_AF"
## [93] "gnomAD_EAS_AF" "gnomAD_FIN_AF"
## [95] "gnomAD_NFE_AF" "gnomAD_OTH_AF"
## [97] "gnomAD_SAS_AF" "MAX_AF"
## [99] "MAX_AF_POPS" "gnomAD_non_cancer_AF"
## [101] "gnomAD_non_cancer_AFR_AF" "gnomAD_non_cancer_AMI_AF"
## [103] "gnomAD_non_cancer_AMR_AF" "gnomAD_non_cancer_ASJ_AF"
## [105] "gnomAD_non_cancer_EAS_AF" "gnomAD_non_cancer_FIN_AF"
## [107] "gnomAD_non_cancer_MID_AF" "gnomAD_non_cancer_NFE_AF"
## [109] "gnomAD_non_cancer_OTH_AF" "gnomAD_non_cancer_SAS_AF"
## [111] "gnomAD_non_cancer_MAX_AF_adj" "gnomAD_non_cancer_MAX_AF_POPS_adj"
## [113] "CLIN_SIG" "SOMATIC"
## [115] "PUBMED" "TRANSCRIPTION_FACTORS"
## [117] "MOTIF_NAME" "MOTIF_POS"
## [119] "HIGH_INF_POS" "MOTIF_SCORE_CHANGE"
## [121] "miRNA" "IMPACT"
## [123] "PICK" "VARIANT_CLASS"
## [125] "TSL" "HGVS_OFFSET"
## [127] "PHENO" "GENE_PHENO"
## [129] "CONTEXT" "tumor_bam_uuid"
## [131] "normal_bam_uuid" "case_id"
## [133] "GDC_FILTER" "COSMIC"
## [135] "hotspot" "RNA_Support"
## [137] "RNA_depth" "RNA_ref_count"
## [139] "RNA_alt_count" "callers"head(mut_data)## Hugo_Symbol Entrez_Gene_Id Center NCBI_Build Chromosome Start_Position
## 1 SCNN1D 6339 BI GRCh38 chr1 1291262
## 2 CEP104 9731 BI GRCh38 chr1 3833942
## 3 NPHP4 261734 BI GRCh38 chr1 5933224
## 4 SH2D5 400745 BI GRCh38 chr1 20724174
## 5 PUM1 9698 BI GRCh38 chr1 30953717
## 6 HDAC1 3065 BI GRCh38 chr1 32331497
## End_Position Strand Variant_Classification Variant_Type Reference_Allele
## 1 1291262 + Silent SNP G
## 2 3833942 + Missense_Mutation SNP C
## 3 5933224 + Silent SNP G
## 4 20724174 + Silent SNP G
## 5 30953717 + Missense_Mutation SNP G
## 6 32331497 + Missense_Mutation SNP G
## Tumor_Seq_Allele1 Tumor_Seq_Allele2 dbSNP_RS dbSNP_Val_Status
## 1 G A NA
## 2 C G NA
## 3 G A NA
## 4 G A rs747513400 NA
## 5 G A NA
## 6 G A NA
## Tumor_Sample_Barcode Matched_Norm_Sample_Barcode
## 1 TCGA-CV-A6JM-01A-11D-A31L-08 TCGA-CV-A6JM-10A-01D-A31J-08
## 2 TCGA-CV-A6JM-01A-11D-A31L-08 TCGA-CV-A6JM-10A-01D-A31J-08
## 3 TCGA-CV-A6JM-01A-11D-A31L-08 TCGA-CV-A6JM-10A-01D-A31J-08
## 4 TCGA-CV-A6JM-01A-11D-A31L-08 TCGA-CV-A6JM-10A-01D-A31J-08
## 5 TCGA-CV-A6JM-01A-11D-A31L-08 TCGA-CV-A6JM-10A-01D-A31J-08
## 6 TCGA-CV-A6JM-01A-11D-A31L-08 TCGA-CV-A6JM-10A-01D-A31J-08
## Match_Norm_Seq_Allele1 Match_Norm_Seq_Allele2 Tumor_Validation_Allele1
## 1 NA NA NA
## 2 NA NA NA
## 3 NA NA NA
## 4 NA NA NA
## 5 NA NA NA
## 6 NA NA NA
## Tumor_Validation_Allele2 Match_Norm_Validation_Allele1
## 1 NA NA
## 2 NA NA
## 3 NA NA
## 4 NA NA
## 5 NA NA
## 6 NA NA
## Match_Norm_Validation_Allele2 Verification_Status Validation_Status
## 1 NA NA NA
## 2 NA NA NA
## 3 NA NA NA
## 4 NA NA NA
## 5 NA NA NA
## 6 NA NA NA
## Mutation_Status Sequencing_Phase Sequence_Source Validation_Method Score
## 1 Somatic NA NA NA NA
## 2 Somatic NA NA NA NA
## 3 Somatic NA NA NA NA
## 4 Somatic NA NA NA NA
## 5 Somatic NA NA NA NA
## 6 Somatic NA NA NA NA
## BAM_File Sequencer Tumor_Sample_UUID
## 1 NA NA 7a8ba569-fd0e-4082-9584-45a4b35ce972
## 2 NA NA 7a8ba569-fd0e-4082-9584-45a4b35ce972
## 3 NA NA 7a8ba569-fd0e-4082-9584-45a4b35ce972
## 4 NA NA 7a8ba569-fd0e-4082-9584-45a4b35ce972
## 5 NA NA 7a8ba569-fd0e-4082-9584-45a4b35ce972
## 6 NA NA 7a8ba569-fd0e-4082-9584-45a4b35ce972
## Matched_Norm_Sample_UUID HGVSc HGVSp HGVSp_Short
## 1 1d09c286-6455-421e-8043-261a6060cb8d c.1569G>A p.Gln523= p.Q523=
## 2 1d09c286-6455-421e-8043-261a6060cb8d c.1579G>C p.Glu527Gln p.E527Q
## 3 1d09c286-6455-421e-8043-261a6060cb8d c.1225C>T p.Leu409= p.L409=
## 4 1d09c286-6455-421e-8043-261a6060cb8d c.708C>T p.Arg236= p.R236=
## 5 1d09c286-6455-421e-8043-261a6060cb8d c.2588C>T p.Ser863Phe p.S863F
## 6 1d09c286-6455-421e-8043-261a6060cb8d c.1003G>A p.Glu335Lys p.E335K
## Transcript_ID Exon_Number t_depth t_ref_count t_alt_count n_depth
## 1 ENST00000338555 15/15 15 7 8 11
## 2 ENST00000378230 12/22 63 46 17 71
## 3 ENST00000378156 10/30 69 46 23 72
## 4 ENST00000444387 7/10 127 84 42 128
## 5 ENST00000257075 15/22 168 148 20 169
## 6 ENST00000373548 10/14 79 49 30 73
## n_ref_count n_alt_count
## 1 NA NA
## 2 NA NA
## 3 NA NA
## 4 NA NA
## 5 NA NA
## 6 NA NA
## all_effects
## 1 SCNN1D,synonymous_variant,p.Q523=,ENST00000338555,,c.1569G>A,LOW,,,,1;SCNN1D,synonymous_variant,p.Q687=,ENST00000379116,NM_001130413.4,c.2061G>A,LOW,YES,,,1;SCNN1D,synonymous_variant,p.Q523=,ENST00000400928,,c.1569G>A,LOW,,,,1;SCNN1D,synonymous_variant,p.Q589=,ENST00000325425,,c.1767G>A,LOW,,,,1;ACAP3,downstream_gene_variant,,ENST00000353662,,,MODIFIER,,,,-1;ACAP3,downstream_gene_variant,,ENST00000354700,NM_030649.3,,MODIFIER,YES,,,-1;SCNN1D,downstream_gene_variant,,ENST00000379099,,,MODIFIER,,,,1;MIR6726,downstream_gene_variant,,ENST00000613751,,,MODIFIER,YES,,,-1;SCNN1D,3_prime_UTR_variant,,ENST00000379101,,c.*980G>A,MODIFIER,,,,1;ACAP3,downstream_gene_variant,,ENST00000467278,,,MODIFIER,,,,-1;ACAP3,downstream_gene_variant,,ENST00000470659,,,MODIFIER,,,,-1;ACAP3,downstream_gene_variant,,ENST00000492936,,,MODIFIER,,,,-1
## 2 CEP104,missense_variant,p.E527Q,ENST00000674623,,c.1579G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;CEP104,missense_variant,p.E533Q,ENST00000676052,,c.1597G>C,MODERATE,,deleterious(0),possibly_damaging(0.809),-1;CEP104,missense_variant,p.E527Q,ENST00000378230,NM_014704.4,c.1579G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;CEP104,missense_variant,p.E527Q,ENST00000675666,,c.1579G>C,MODERATE,YES,deleterious(0),possibly_damaging(0.862),-1;CEP104,missense_variant,p.E527Q,ENST00000674558,,c.1579G>C,MODERATE,,deleterious(0),probably_damaging(0.997),-1;CEP104,missense_variant,p.E461Q,ENST00000675677,,c.1381G>C,MODERATE,,deleterious(0.01),possibly_damaging(0.658),-1;CEP104,missense_variant,p.E469Q,ENST00000675375,,c.1405G>C,MODERATE,,deleterious(0),possibly_damaging(0.877),-1;CEP104,missense_variant,p.E469Q,ENST00000674544,,c.1405G>C,MODERATE,,deleterious(0),possibly_damaging(0.809),-1;CEP104,missense_variant,p.E527Q,ENST00000461667,,c.1579G>C,MODERATE,,deleterious(0),possibly_damaging(0.809),-1;CEP104,missense_variant,p.E527Q,ENST00000428079,,c.1579G>C,MODERATE,,deleterious(0),possibly_damaging(0.809),-1;CEP104,missense_variant,p.E527Q,ENST00000494653,,c.1579G>C,MODERATE,,deleterious(0),probably_damaging(0.973),-1;CEP104,non_coding_transcript_exon_variant,,ENST00000438539,,n.626G>C,MODIFIER,,,,-1;CEP104,non_coding_transcript_exon_variant,,ENST00000460038,,n.484G>C,MODIFIER,,,,-1;CEP104,missense_variant,p.E527Q,ENST00000676009,,c.1579G>C,MODERATE,,deleterious(0),probably_damaging(0.95),-1;CEP104,missense_variant,p.E469Q,ENST00000675200,,c.1405G>C,MODERATE,,deleterious(0.01),possibly_damaging(0.757),-1;CEP104,3_prime_UTR_variant,,ENST00000675108,,c.*1495G>C,MODIFIER,,,,-1;CEP104,3_prime_UTR_variant,,ENST00000674985,,c.*437G>C,MODIFIER,,,,-1;CEP104,3_prime_UTR_variant,,ENST00000675750,,c.*908G>C,MODIFIER,,,,-1;CEP104,non_coding_transcript_exon_variant,,ENST00000675966,,n.3251G>C,MODIFIER,,,,-1;CEP104,non_coding_transcript_exon_variant,,ENST00000674879,,n.2515G>C,MODIFIER,,,,-1;CEP104,non_coding_transcript_exon_variant,,ENST00000675334,,n.1383G>C,MODIFIER,,,,-1;CEP104,upstream_gene_variant,,ENST00000495701,,,MODIFIER,,,,-1;CEP104,downstream_gene_variant,,ENST00000675520,,,MODIFIER,,,,-1
## 3 NPHP4,synonymous_variant,p.L409=,ENST00000378156,NM_001291594.2&NM_001291593.2&NM_015102.5,c.1225C>T,LOW,YES,,,-1;NPHP4,synonymous_variant,p.L409=,ENST00000622020,,c.1225C>T,LOW,,,,-1;NPHP4,non_coding_transcript_exon_variant,,ENST00000478423,,n.1127C>T,MODIFIER,,,,-1;NPHP4,synonymous_variant,p.L409=,ENST00000489180,,c.1225C>T,LOW,,,,-1;NPHP4,3_prime_UTR_variant,,ENST00000378169,,c.*299C>T,MODIFIER,,,,-1
## 4 SH2D5,synonymous_variant,p.R236=,ENST00000444387,NM_001103161.2,c.708C>T,LOW,YES,,,-1;SH2D5,synonymous_variant,p.R152=,ENST00000375031,NM_001103160.2,c.456C>T,LOW,,,,-1;SH2D5,downstream_gene_variant,,ENST00000447746,,,MODIFIER,,,,-1;SH2D5,downstream_gene_variant,,ENST00000517430,,,MODIFIER,,,,-1;SH2D5,downstream_gene_variant,,ENST00000518294,,,MODIFIER,,,,-1;SH2D5,downstream_gene_variant,,ENST00000519434,,,MODIFIER,,,,-1;SH2D5,non_coding_transcript_exon_variant,,ENST00000460804,,n.439C>T,MODIFIER,,,,-1
## 5 PUM1,missense_variant,p.S863F,ENST00000426105,NM_001020658.2,c.2588C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S864F,ENST00000373747,,c.2591C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S863F,ENST00000257075,NM_014676.3,c.2588C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S621F,ENST00000424085,,c.1862C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S802F,ENST00000525843,,c.2405C>T,MODERATE,,deleterious(0),probably_damaging(0.999),-1;PUM1,missense_variant,p.S899F,ENST00000373741,,c.2696C>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S837F,ENST00000440538,,c.2510C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S804F,ENST00000373742,,c.2411C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S575F,ENST00000498419,,c.1724C>T,MODERATE,,deleterious(0),probably_damaging(1),-1;PUM1,missense_variant,p.S14F,ENST00000529846,,c.41C>T,MODERATE,,deleterious(0),probably_damaging(0.983),-1;PUM1,missense_variant,p.S10F,ENST00000525997,,c.29C>T,MODERATE,,deleterious(0),probably_damaging(0.997),-1;PUM1,3_prime_UTR_variant,,ENST00000527498,,c.*28C>T,MODIFIER,,,,-1
## 6 HDAC1,missense_variant,p.E335K,ENST00000373548,NM_004964.3,c.1003G>A,MODERATE,YES,tolerated(0.05),possibly_damaging(0.534),1;MARCKSL1,downstream_gene_variant,,ENST00000329421,NM_023009.7,,MODIFIER,YES,,,-1;HDAC1,downstream_gene_variant,,ENST00000428704,,,MODIFIER,,,,1;HDAC1,non_coding_transcript_exon_variant,,ENST00000490081,,n.856G>A,MODIFIER,,,,1;HDAC1,non_coding_transcript_exon_variant,,ENST00000482310,,n.694G>A,MODIFIER,,,,1;HDAC1,downstream_gene_variant,,ENST00000463172,,,MODIFIER,,,,1;HDAC1,downstream_gene_variant,,ENST00000472928,,,MODIFIER,,,,1;HDAC1,downstream_gene_variant,,ENST00000481281,,,MODIFIER,,,,1;HDAC1,non_coding_transcript_exon_variant,,ENST00000476391,,n.1372G>A,MODIFIER,,,,1;HDAC1,upstream_gene_variant,,ENST00000471488,,,MODIFIER,,,,1;HDAC1,downstream_gene_variant,,ENST00000484305,,,MODIFIER,,,,1
## Allele Gene Feature Feature_type One_Consequence
## 1 A ENSG00000162572 ENST00000338555 Transcript synonymous_variant
## 2 G ENSG00000116198 ENST00000378230 Transcript missense_variant
## 3 A ENSG00000131697 ENST00000378156 Transcript synonymous_variant
## 4 A ENSG00000189410 ENST00000444387 Transcript synonymous_variant
## 5 A ENSG00000134644 ENST00000257075 Transcript missense_variant
## 6 A ENSG00000116478 ENST00000373548 Transcript missense_variant
## Consequence cDNA_position CDS_position Protein_position Amino_acids
## 1 synonymous_variant 2713/3475 1569/1917 523/638 Q
## 2 missense_variant 1916/6431 1579/2778 527/925 E/Q
## 3 synonymous_variant 1445/4955 1225/4281 409/1426 L
## 4 synonymous_variant 1273/3898 708/1272 236/423 R
## 5 missense_variant 2682/5360 2588/3561 863/1186 S/F
## 6 missense_variant 1090/2118 1003/1449 335/482 E/K
## Codons Existing_variation DISTANCE TRANSCRIPT_STRAND SYMBOL
## 1 caG/caA COSV100330268 NA 1 SCNN1D
## 2 Gag/Cag COSV100986731 NA -1 CEP104
## 3 Ctg/Ttg COSV65393728 NA -1 NPHP4
## 4 cgC/cgT rs747513400;COSV100903899 NA -1 SH2D5
## 5 tCc/tTc COSV99928933 NA -1 PUM1
## 6 Gaa/Aaa COSV100269676 NA 1 HDAC1
## SYMBOL_SOURCE HGNC_ID BIOTYPE CANONICAL CCDS ENSP
## 1 HGNC HGNC:10601 protein_coding ENSP00000339504
## 2 HGNC HGNC:24866 protein_coding CCDS30571.1 ENSP00000367476
## 3 HGNC HGNC:19104 protein_coding YES CCDS44052.1 ENSP00000367398
## 4 HGNC HGNC:28819 protein_coding YES CCDS44080.1 ENSP00000406026
## 5 HGNC HGNC:14957 protein_coding CCDS338.1 ENSP00000257075
## 6 HGNC HGNC:4852 protein_coding YES CCDS360.1 ENSP00000362649
## SWISSPROT TREMBL UNIPARC UNIPROT_ISOFORM
## 1 P51172.169 UPI000013E180 P51172-1
## 2 O60308.148 UPI0000139AA8 O60308-1
## 3 O75161.161 UPI00001303E5 O75161-1
## 4 Q6ZV89.140 UPI0000EE70C3 Q6ZV89-1
## 5 Q14671.182 UPI000014FCE2 Q14671-1
## 6 Q13547.233 Q6IT96.143 UPI0000035528
## RefSeq MANE APPRIS FLAGS
## 1 A2 NA
## 2 NM_014704.4 NM_014704.4 P2 NA
## 3 NM_001291594.2;NM_001291593.2;NM_015102.5 NM_015102.5 P2 NA
## 4 NM_001103161.2 NM_001103161.2 P1 NA
## 5 NM_014676.3 A1 NA
## 6 NM_004964.3 NM_004964.3 P1 NA
## SIFT PolyPhen EXON INTRON
## 1 15/15
## 2 deleterious(0) probably_damaging(0.997) 12/22
## 3 10/30
## 4 7/10
## 5 deleterious(0) probably_damaging(1) 15/22
## 6 tolerated(0.05) possibly_damaging(0.534) 10/14
## DOMAINS
## 1 PANTHER:PTHR11690:SF132;PANTHER:PTHR11690;Pfam:PF00858;Gene3D:1.10.287.770;TIGRFAM:TIGR00859;Prints:PR01078
## 2 PDB-ENSP_mappings:5lph.A;PDB-ENSP_mappings:5lph.B;PANTHER:PTHR13371;PANTHER:PTHR13371:SF0;Gene3D:1.25.10.10;SMART:SM01349;Superfamily:SSF48371
## 3 PANTHER:PTHR31043
## 4 PANTHER:PTHR15832;PANTHER:PTHR15832:SF3
## 5 PDB-ENSP_mappings:1ib2.A;PDB-ENSP_mappings:1m8w.A;PDB-ENSP_mappings:1m8w.B;PDB-ENSP_mappings:1m8x.A;PDB-ENSP_mappings:1m8x.B;PDB-ENSP_mappings:1m8y.A;PDB-ENSP_mappings:1m8y.B;PDB-ENSP_mappings:1m8z.A;PDB-ENSP_mappings:2yjy.A;PDB-ENSP_mappings:2yjy.B;PDB-ENSP_mappings:3bsb.A;PDB-ENSP_mappings:3bsb.B;PDB-ENSP_mappings:3bsx.A;PDB-ENSP_mappings:3bsx.B;PDB-ENSP_mappings:3q0l.A;PDB-ENSP_mappings:3q0l.B;PDB-ENSP_mappings:3q0m.A;PDB-ENSP_mappings:3q0m.B;PDB-ENSP_mappings:3q0n.A;PDB-ENSP_mappings:3q0n.B;PDB-ENSP_mappings:3q0o.A;PDB-ENSP_mappings:3q0o.B;PDB-ENSP_mappings:3q0p.A;PDB-ENSP_mappings:3q0p.B;PDB-ENSP_mappings:5ykh.A;PDB-ENSP_mappings:5yki.A;PROSITE_profiles:PS50302;PROSITE_profiles:PS50303;CDD:cd07920;PANTHER:PTHR12537:SF1;PANTHER:PTHR12537;Pfam:PF00806;Gene3D:1.25.10.10;SMART:SM00025;Superfamily:SSF48371
## 6 PDB-ENSP_mappings:4bkx.B;PDB-ENSP_mappings:5icn.B;CDD:cd10010;PANTHER:PTHR10625:SF191;PANTHER:PTHR10625;PIRSF:PIRSF037913;Gene3D:3.40.800.20;Superfamily:SSF52768
## X1000G_AF X1000G_AFR_AF X1000G_AMR_AF X1000G_EAS_AF X1000G_EUR_AF
## 1 NA NA NA NA NA
## 2 NA NA NA NA NA
## 3 NA NA NA NA NA
## 4 NA NA NA NA NA
## 5 NA NA NA NA NA
## 6 NA NA NA NA NA
## X1000G_SAS_AF ESP_AA_AF ESP_EA_AF gnomAD_AF gnomAD_AFR_AF gnomAD_AMR_AF
## 1 NA NA NA NA NA NA
## 2 NA NA NA NA NA NA
## 3 NA NA NA NA NA NA
## 4 NA NA NA 2.831e-05 0 0
## 5 NA NA NA NA NA NA
## 6 NA NA NA NA NA NA
## gnomAD_ASJ_AF gnomAD_EAS_AF gnomAD_FIN_AF gnomAD_NFE_AF gnomAD_OTH_AF
## 1 NA NA NA NA NA
## 2 NA NA NA NA NA
## 3 NA NA NA NA NA
## 4 0 0 0 5.39e-05 0.0001661
## 5 NA NA NA NA NA
## 6 NA NA NA NA NA
## gnomAD_SAS_AF MAX_AF MAX_AF_POPS gnomAD_non_cancer_AF
## 1 NA NA NA
## 2 NA NA NA
## 3 NA NA NA
## 4 0 0.0001661 gnomAD_OTH 6.75886e-06
## 5 NA NA NA
## 6 NA NA NA
## gnomAD_non_cancer_AFR_AF gnomAD_non_cancer_AMI_AF gnomAD_non_cancer_AMR_AF
## 1 NA NA NA
## 2 NA NA NA
## 3 NA NA NA
## 4 0 0 0
## 5 NA NA NA
## 6 NA NA NA
## gnomAD_non_cancer_ASJ_AF gnomAD_non_cancer_EAS_AF gnomAD_non_cancer_FIN_AF
## 1 NA NA NA
## 2 NA NA NA
## 3 NA NA NA
## 4 0 0 0
## 5 NA NA NA
## 6 NA NA NA
## gnomAD_non_cancer_MID_AF gnomAD_non_cancer_NFE_AF gnomAD_non_cancer_OTH_AF
## 1 NA NA NA
## 2 NA NA NA
## 3 NA NA NA
## 4 0 1.54302e-05 0
## 5 NA NA NA
## 6 NA NA NA
## gnomAD_non_cancer_SAS_AF gnomAD_non_cancer_MAX_AF_adj
## 1 NA NA
## 2 NA NA
## 3 NA NA
## 4 0 NA
## 5 NA NA
## 6 NA NA
## gnomAD_non_cancer_MAX_AF_POPS_adj CLIN_SIG SOMATIC PUBMED
## 1 NA 1 NA
## 2 NA 1 NA
## 3 NA 1 NA
## 4 NA 0;1 NA
## 5 NA 1 NA
## 6 NA 1 NA
## TRANSCRIPTION_FACTORS MOTIF_NAME MOTIF_POS HIGH_INF_POS MOTIF_SCORE_CHANGE
## 1 NA NA NA NA NA
## 2 NA NA NA NA NA
## 3 NA NA NA NA NA
## 4 NA NA NA NA NA
## 5 NA NA NA NA NA
## 6 NA NA NA NA NA
## miRNA IMPACT PICK VARIANT_CLASS TSL HGVS_OFFSET PHENO GENE_PHENO
## 1 NA LOW NA SNV 2 NA 1 NA
## 2 NA MODERATE NA SNV 5 NA 1 1
## 3 NA LOW 1 SNV 1 NA 1 1
## 4 NA LOW 1 SNV 2 NA 0;1 NA
## 5 NA MODERATE NA SNV 1 NA 1 1
## 6 NA MODERATE 1 SNV 1 NA 1 NA
## CONTEXT tumor_bam_uuid
## 1 CCGCAGCTGCT 3b5ffb9f-1510-4608-b998-4a520f32ac74
## 2 CCTCTCCACAC 3b5ffb9f-1510-4608-b998-4a520f32ac74
## 3 CTGCAGAGGCA 3b5ffb9f-1510-4608-b998-4a520f32ac74
## 4 TTCTTGCGCAC 3b5ffb9f-1510-4608-b998-4a520f32ac74
## 5 ACCTGGACCCA 3b5ffb9f-1510-4608-b998-4a520f32ac74
## 6 ACTTTGAATAC 3b5ffb9f-1510-4608-b998-4a520f32ac74
## normal_bam_uuid case_id
## 1 e547d38f-e264-4c45-8051-48a5c815d14e 08c95e8f-aa2f-4163-ac43-096053ec6886
## 2 e547d38f-e264-4c45-8051-48a5c815d14e 08c95e8f-aa2f-4163-ac43-096053ec6886
## 3 e547d38f-e264-4c45-8051-48a5c815d14e 08c95e8f-aa2f-4163-ac43-096053ec6886
## 4 e547d38f-e264-4c45-8051-48a5c815d14e 08c95e8f-aa2f-4163-ac43-096053ec6886
## 5 e547d38f-e264-4c45-8051-48a5c815d14e 08c95e8f-aa2f-4163-ac43-096053ec6886
## 6 e547d38f-e264-4c45-8051-48a5c815d14e 08c95e8f-aa2f-4163-ac43-096053ec6886
## GDC_FILTER COSMIC hotspot RNA_Support RNA_depth RNA_ref_count
## 1 N Unknown NA NA
## 2 N Unknown NA NA
## 3 COSM681621 N Unknown NA NA
## 4 N Unknown NA NA
## 5 N Unknown NA NA
## 6 N Unknown NA NA
## RNA_alt_count callers
## 1 NA muse;mutect2;varscan2
## 2 NA muse;mutect2;varscan2
## 3 NA muse;mutect2;varscan2
## 4 NA muse;mutect2;varscan2
## 5 NA muse;mutect2;varscan2
## 6 NA muse;mutect2;varscan2# List of genes that are mutated in the particular patient
unique(mut_data$Hugo_Symbol)## [1] "SCNN1D" "CEP104" "NPHP4" "SH2D5" "PUM1"
## [6] "HDAC1" "DLGAP3" "MAGOH" "HRNR" "NUP210L"
## [11] "ATP8B2" "GON4L" "OR10K2" "HSPA6" "DDR2"
## [16] "SUCO" "KDM5B" "CNTN2" "USH2A" "MIA3"
## [21] "OBSCN" "H3-4" "TAF5L" "OR2M5" "LAPTM4A"
## [26] "ASXL2" "PPM1G" "ABCG8" "PAPOLG" "XPO1"
## [31] "VPS54" "M1AP" "SEMA4F" "NOSTRIN" "SLC25A12"
## [36] "NEUROD1" "ITGAV" "CASP8" "CRYGC" "CUL3"
## [41] "DAW1" "SPHKAP" "ECEL1" "ASB1" "FANCD2"
## [46] "MYRIP" "NKTR" "GXYLT2" "SIDT1" "CPA3"
## [51] "NLGN1" "NAALADL2" "PIK3CA" "CCDC39" "RFC4"
## [56] "SORCS2" "SLC4A4" "PPEF2" "MEPE" "GATB"
## [61] "NEK1" "PLEKHG4B" "TRIO" "NIPBL" "SLC38A9"
## [66] "SPOCK1" "PCDHA8" "PCDHAC1" "PCDHGA5" "KIF4B"
## [71] "PROP1" "MGAT4B" "ZBED9" "SKIV2L" "ITPR3"
## [76] "MAD2L1BP" "LCA5" "ZNF292" "COQ3" "FIG4"
## [81] "GRM1" "RNASET2" "ERMARD" "FSCN1" "SUGCT"
## [86] "CFTR" "KEL" "CASP2" "KCTD9" "ZMAT4"
## [91] "GINS4" "CLVS1" "FABP4" "RIMS2" "KCNV1"
## [96] "CSMD3" "EXT1" "KLHL38" "ADCY8" "GLI4"
## [101] "PLEC" "BNC2" "CDKN2A" "CREB3" "C9orf40"
## [106] "OSTF1" "TMEFF1" "OR1L4" "NOTCH1" "UCMA"
## [111] "ITGA8" "SVIL" "ZNF32" "AGAP7P" "OGDHL"
## [116] "ANK3" "EGR2" "MYPN" "SFTPA2" "RNLS"
## [121] "CPEB3" "TECTB" "PNLIPRP3" "PRLHR" "CTBP2"
## [126] "BCCIP" "B4GALNT4" "MUC5B" "DENND5A" "ALX4"
## [131] "LRP4" "TRIM48" "DDB1" "TUT1" "MTA2"
## [136] "SLC22A8" "ATL3" "OTUB1" "STIP1" "RASGRP2"
## [141] "AP000769.3"table(mut_data$Variant_Type)##
## DEL INS SNP
## 1 2 1 144table(mut_data$Variant_Classification)##
## 5Flank\tSNP\tC\tC\tT\trs767238952\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\t\t\t\tENST00000611300\t\t83\t65\t18\t73\t\t\tAP000769.3,upstream_gene_variant,,ENST00000611300,,,MODIFIER,YES,,,1;AP000769.5,downstream_gene_variant,,ENST00000618249,,,MODIFIER,YES,,,1;MALAT1,non_coding_transcript_exon_variant,,ENST00000534336,,n.5837C>T,MODIFIER,YES,,,1;MALAT1,non_coding_transcript_exon_variant,,ENST00000619449,,n.4861C>T,MODIFIER,,,,1;MALAT1,non_coding_transcript_exon_variant,,ENST00000508832,,n.1508C>T,MODIFIER,,,,1;MALAT1,intron_variant,,ENST00000616527,,n.435-728C>T,MODIFIER,,,,1;MALAT1,intron_variant,,ENST00000618925,,n.393-131C>T,MODIFIER,,,,1;MALAT1,downstream_gene_variant,,ENST00000544868,,,MODIFIER,,,,1;MALAT1,downstream_gene_variant,,ENST00000610481,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000610851,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000612781,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000613376,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000616691,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000617489,,,MODIFIER,,,,1;MALAT1,downstream_gene_variant,,ENST00000617791,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000618132,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000618227,,,MODIFIER,,,,1;MALAT1,upstream_gene_variant,,ENST00000620465,,,MODIFIER,,,,1;MALAT1,downstream_gene_variant,,ENST00000620902,,,MODIFIER,,,,1\tT\tENSG00000274072\tENST00000611300\tTranscript\tupstream_gene_variant\tupstream_gene_variant\t\t\t\t\t\trs767238952\t2519\t1\tAP000769.3\tClone_based_ensembl_gene\t\tsRNA\tYES\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1.816e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t3.827e-05\t0.0\t0.0\t3.827e-05\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tMODIFIER\t\tSNV\t\t\t\t\tTCATTCAAAAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPCNX3\t399909\tBI\tGRCh38\tchr11\t65616380\t65616380\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.69C>T\tp.Phe23=\tp.F23=\tENST00000355703\t1/35\t56\t40\t16\t26\t\t\tPCNX3,synonymous_variant,p.F23=,ENST00000355703,NM_032223.3,c.69C>T,LOW,YES,,,1;MAP3K11,upstream_gene_variant,,ENST00000309100,NM_002419.4,,MODIFIER,YES,,,-1;MAP3K11,upstream_gene_variant,,ENST00000526293,,,MODIFIER,,,,-1;MAP3K11,upstream_gene_variant,,ENST00000529839,,,MODIFIER,,,,-1;PCNX3,upstream_gene_variant,,ENST00000531045,,,MODIFIER,,,,1;MAP3K11,upstream_gene_variant,,ENST00000524856,,,MODIFIER,,,,-1;MAP3K11,upstream_gene_variant,,ENST00000527304,,,MODIFIER,,,,-1\tT\tENSG00000197136\tENST00000355703\tTranscript\tsynonymous_variant\tsynonymous_variant\t608/7105\t69/6105\t23/2034\tF\tttC/ttT\tCOSV100482731\t\t1\tPCNX3\tHGNC\tHGNC:18760\tprotein_coding\tYES\tCCDS44650.1\tENSP00000347931\tQ9H6A9.116\t\tUPI0000405B22\tQ9H6A9-1\tNM_032223.3\t\tP1\t\t\t\t1/35\t\tPANTHER:PTHR12372;PANTHER:PTHR12372:SF4\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t5\t\t1\t\tTTCTTCGACCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nC11orf24\t53838\tBI\tGRCh38\tchr11\t68262888\t68262888\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.107G>C\tp.Gly36Ala\tp.G36A\tENST00000304271\t4/4\t161\t140\t21\t51\t\t\tC11orf24,missense_variant,p.G36A,ENST00000304271,NM_022338.4,c.107G>C,MODERATE,YES,tolerated(0.34),benign(0.005),-1;C11orf24,missense_variant,p.G36A,ENST00000533310,NM_001300913.2,c.107G>C,MODERATE,,tolerated(0.37),benign(0.005),-1;C11orf24,downstream_gene_variant,,ENST00000527280,,,MODIFIER,,,,-1;C11orf24,non_coding_transcript_exon_variant,,ENST00000530166,,n.516G>C,MODIFIER,,,,-1;C11orf24,intron_variant,,ENST00000531745,,n.111+357G>C,MODIFIER,,,,-1;C11orf24,downstream_gene_variant,,ENST00000529590,,,MODIFIER,,,,-1;C11orf24,downstream_gene_variant,,ENST00000532534,,,MODIFIER,,,,-1;C11orf24,downstream_gene_variant,,ENST00000532969,,,MODIFIER,,,,-1;C11orf24,downstream_gene_variant,,ENST00000529339,,,MODIFIER,,,,-1\tG\tENSG00000171067\tENST00000304271\tTranscript\tmissense_variant\tmissense_variant\t521/2071\t107/1350\t36/449\tG/A\tgGa/gCa\tCOSV100422705\t\t-1\tC11orf24\tHGNC\tHGNC:1174\tprotein_coding\tYES\tCCDS8180.1\tENSP00000307264\tQ96F05.118\tA0A024R5K9.49\tUPI000006E42A\t\tNM_022338.4\tNM_022338.4\tP4\t\ttolerated(0.34)\tbenign(0.005)\t4/4\t\tPANTHER:PTHR16021;PANTHER:PTHR16021:SF9;Pfam:PF17823\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCTAATCCCTTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPGM2L1\t283209\tBI\tGRCh38\tchr11\t74345563\t74345563\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1124G>A\tp.Arg375Lys\tp.R375K\tENST00000298198\t9/14\t103\t87\t16\t38\t\t\tPGM2L1,missense_variant,p.R375K,ENST00000298198,NM_173582.6,c.1124G>A,MODERATE,YES,tolerated(0.73),benign(0),-1\tT\tENSG00000165434\tENST00000298198\tTranscript\tmissense_variant\tmissense_variant\t1396/8477\t1124/1869\t375/622\tR/K\taGa/aAa\tCOSV99995209\t\t-1\tPGM2L1\tHGNC\tHGNC:20898\tprotein_coding\tYES\tCCDS8231.1\tENSP00000298198\tQ6PCE3.144\t\tUPI0000072053\t\tNM_173582.6\tNM_173582.6\tP1\t\ttolerated(0.73)\tbenign(0)\t9/14\t\tCDD:cd05799;PANTHER:PTHR45745;PANTHER:PTHR45745:SF2;Gene3D:3.40.120.10;Pfam:PF02880;Superfamily:SSF53738\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCATTTCTTGAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPAK1\t5058\tBI\tGRCh38\tchr11\t77337327\t77337327\t+\tMissense_Mutation\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1213C>A\tp.Leu405Ile\tp.L405I\tENST00000356341\t12/15\t18\t5\t13\t18\t\t\tPAK1,missense_variant,p.L405I,ENST00000356341,NM_001376273.1&NM_001376301.1&NM_001376290.1&NM_002576.5&NM_001376281.1&NM_001376283.1&NM_001376276.1&NM_001376280.1&NM_001376284.1&NM_001376282.1&NM_001376277.1&NM_001376293.1&NM_001376278.1&NM_001376303.1&NM_001376295.1&NM_001376291.1&NM_001376292.1&NM_001376274.1&NM_001376272.1&NM_001376279.1&NM_001376275.1&NM_001376294.1&NM_001376286.1&NM_001376287.1&NM_001376285.1,c.1213C>A,MODERATE,,deleterious(0.04),probably_damaging(0.916),-1;PAK1,missense_variant,p.L405I,ENST00000530617,NM_001376288.1,c.1213C>A,MODERATE,,tolerated(0.07),probably_damaging(0.949),-1;PAK1,missense_variant,p.L405I,ENST00000278568,NM_001376268.1&NM_001128620.2&NM_001376270.1&NM_001376289.1&NM_001376269.1&NM_001376271.1,c.1213C>A,MODERATE,YES,tolerated(0.11),probably_damaging(0.968),-1;PAK1,missense_variant,p.L307I,ENST00000528203,NM_001376304.1&NM_001376305.1&NM_001376302.1,c.919C>A,MODERATE,,tolerated(0.11),probably_damaging(0.988),-1;PAK1,missense_variant,p.L127I,ENST00000533285,,c.379C>A,MODERATE,,tolerated_low_confidence(0.07),probably_damaging(0.97),-1;PAK1,non_coding_transcript_exon_variant,,ENST00000525542,,n.433C>A,MODIFIER,,,,-1;PAK1,3_prime_UTR_variant,,ENST00000527535,,c.*309C>A,MODIFIER,,,,-1;PAK1,non_coding_transcript_exon_variant,,ENST00000532991,,n.636C>A,MODIFIER,,,,-1;PAK1,intron_variant,,ENST00000527457,,c.*60-1045C>A,MODIFIER,,,,-1;PAK1,intron_variant,,ENST00000532711,,n.280-1045C>A,MODIFIER,,,,-1\tT\tENSG00000149269\tENST00000356341\tTranscript\tmissense_variant\tmissense_variant\t1777/3459\t1213/1638\t405/545\tL/I\tCta/Ata\tCOSV99583948\t\t-1\tPAK1\tHGNC\tHGNC:8590\tprotein_coding\t\tCCDS8250.1\tENSP00000348696\tQ13153.222\tA0A024R5P0.52\tUPI000013ED74\tQ13153-1\tNM_001376273.1;NM_001376301.1;NM_001376290.1;NM_002576.5;NM_001376281.1;NM_001376283.1;NM_001376276.1;NM_001376280.1;NM_001376284.1;NM_001376282.1;NM_001376277.1;NM_001376293.1;NM_001376278.1;NM_001376303.1;NM_001376295.1;NM_001376291.1;NM_001376292.1;NM_001376274.1;NM_001376272.1;NM_001376279.1;NM_001376275.1;NM_001376294.1;NM_001376286.1;NM_001376287.1;NM_001376285.1\tNM_002576.5\tP1\t\tdeleterious(0.04)\tprobably_damaging(0.916)\t12/15\t\tPDB-ENSP_mappings:1f3m.C;PDB-ENSP_mappings:1f3m.D;PDB-ENSP_mappings:1yhv.A;PDB-ENSP_mappings:1yhw.A;PDB-ENSP_mappings:2hy8.1;PDB-ENSP_mappings:3fxz.A;PDB-ENSP_mappings:3fy0.A;PDB-ENSP_mappings:3q4z.A;PDB-ENSP_mappings:3q4z.B;PDB-ENSP_mappings:3q52.A;PDB-ENSP_mappings:3q53.A;PDB-ENSP_mappings:4daw.A;PDB-ENSP_mappings:4eqc.A;PDB-ENSP_mappings:4o0r.A;PDB-ENSP_mappings:4o0r.B;PDB-ENSP_mappings:4o0t.A;PDB-ENSP_mappings:4o0t.B;PDB-ENSP_mappings:4p90.A;PDB-ENSP_mappings:4p90.B;PDB-ENSP_mappings:4zji.A;PDB-ENSP_mappings:4zji.B;PDB-ENSP_mappings:4zji.C;PDB-ENSP_mappings:4zji.D;PDB-ENSP_mappings:4zjj.A;PDB-ENSP_mappings:4zjj.B;PDB-ENSP_mappings:4zjj.C;PDB-ENSP_mappings:4zjj.D;PDB-ENSP_mappings:4zlo.A;PDB-ENSP_mappings:4zlo.B;PDB-ENSP_mappings:4zy4.A;PDB-ENSP_mappings:4zy4.B;PDB-ENSP_mappings:4zy5.A;PDB-ENSP_mappings:4zy5.B;PDB-ENSP_mappings:4zy6.A;PDB-ENSP_mappings:4zy6.B;PDB-ENSP_mappings:5dew.A;PDB-ENSP_mappings:5dew.B;PDB-ENSP_mappings:5dey.A;PDB-ENSP_mappings:5dey.B;PDB-ENSP_mappings:5dfp.A;PDB-ENSP_mappings:5ime.A;PDB-ENSP_mappings:5ime.B;PDB-ENSP_mappings:5kbq.A;PDB-ENSP_mappings:5kbq.B;PDB-ENSP_mappings:5kbr.A;PDB-ENSP_mappings:5kbr.B;PDB-ENSP_mappings:6b16.A;PDB-ENSP_mappings:6b16.B;PROSITE_profiles:PS50011;CDD:cd06654;PANTHER:PTHR45832:SF10;PANTHER:PTHR45832;Pfam:PF00069;Gene3D:1.10.510.10;SMART:SM00220;Superfamily:SSF56112\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t1\tACTTAGCTTGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nGAB2\t9846\tBI\tGRCh38\tchr11\t78250206\t78250206\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.571G>A\tp.Glu191Lys\tp.E191K\tENST00000361507\t3/10\t245\t103\t142\t272\t\t\tGAB2,missense_variant,p.E191K,ENST00000361507,NM_080491.3,c.571G>A,MODERATE,YES,deleterious(0.01),benign(0.073),-1;GAB2,missense_variant,p.E153K,ENST00000340149,NM_012296.3,c.457G>A,MODERATE,,deleterious(0.01),benign(0.073),-1;GAB2,downstream_gene_variant,,ENST00000528886,,,MODIFIER,,,,-1;GAB2,downstream_gene_variant,,ENST00000530915,,,MODIFIER,,,,-1;GAB2,intron_variant,,ENST00000526030,,n.556-23155G>A,MODIFIER,,,,-1\tT\tENSG00000033327\tENST00000361507\tTranscript\tmissense_variant\tmissense_variant\t671/6110\t571/2031\t191/676\tE/K\tGag/Aag\tCOSV100416854\t\t-1\tGAB2\tHGNC\tHGNC:14458\tprotein_coding\tYES\tCCDS8259.1\tENSP00000354952\tQ9UQC2.164\t\tUPI0000073037\tQ9UQC2-1\tNM_080491.3\tNM_080491.3\tP1\t\tdeleterious(0.01)\tbenign(0.073)\t3/10\t\tPANTHER:PTHR45960:SF1;PANTHER:PTHR45960\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t6.799390121159377e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0002138580020982772\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tATACTCCTGAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nDDIAS\t220042\tBI\tGRCh38\tchr11\t82932857\t82932857\t+\tMissense_Mutation\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1519G>T\tp.Val507Phe\tp.V507F\tENST00000329143\t4/4\t25\t8\t17\t14\t\t\tDDIAS,missense_variant,p.V507F,ENST00000533655,NM_145018.4&NM_001363481.2,c.1519G>T,MODERATE,YES,deleterious(0.03),benign(0.057),1;DDIAS,missense_variant,p.V507F,ENST00000329143,,c.1519G>T,MODERATE,,deleterious(0.03),benign(0.057),1;DDIAS,3_prime_UTR_variant,,ENST00000528759,,c.*1038G>T,MODIFIER,,,,1;DDIAS,intron_variant,,ENST00000525361,,c.511+1008G>T,MODIFIER,,,,1;PRCP,intron_variant,,ENST00000534396,,c.-148+24208C>A,MODIFIER,,,,-1;DDIAS,downstream_gene_variant,,ENST00000524921,,,MODIFIER,,,,1;DDIAS,downstream_gene_variant,,ENST00000525388,,,MODIFIER,,,,1;DDIAS,downstream_gene_variant,,ENST00000528262,,,MODIFIER,,,,1;DDIAS,downstream_gene_variant,,ENST00000532277,,,MODIFIER,,,,1;DDIAS,downstream_gene_variant,,ENST00000532589,,,MODIFIER,,,,1;DDIAS,downstream_gene_variant,,ENST00000532764,,,MODIFIER,,,,1;DDIAS,downstream_gene_variant,,ENST00000533750,,,MODIFIER,,,,1;DDIAS,downstream_gene_variant,,ENST00000528189,,,MODIFIER,,,,1\tT\tENSG00000165490\tENST00000329143\tTranscript\tmissense_variant\tmissense_variant\t1569/3367\t1519/2997\t507/998\tV/F\tGtt/Ttt\tCOSV100231438\t\t1\tDDIAS\tHGNC\tHGNC:26351\tprotein_coding\t\tCCDS8263.1\tENSP00000329930\tQ8IXT1.124\t\tUPI00001AF966\tQ8IXT1-1\t\t\t\t\tdeleterious(0.03)\tbenign(0.057)\t4/4\t\tPANTHER:PTHR35537\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tCTAGTGTTGAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;varscan2\nZBTB16\t7704\tBI\tGRCh38\tchr11\t114063633\t114063633\t+\tSilent\tSNP\tC\tC\tA\trs200027612\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.333C>A\tp.Ile111=\tp.I111=\tENST00000335953\t2/7\t29\t9\t20\t39\t\t\tZBTB16,synonymous_variant,p.I111=,ENST00000335953,NM_001354750.2&NM_006006.6&NM_001354751.2&NM_001354752.1,c.333C>A,LOW,YES,,,1;ZBTB16,synonymous_variant,p.I111=,ENST00000392996,NM_001018011.2,c.333C>A,LOW,,,,1;ZBTB16,synonymous_variant,p.I111=,ENST00000544220,,c.333C>A,LOW,,,,1;ZBTB16,synonymous_variant,p.I111=,ENST00000535700,,c.333C>A,LOW,,,,1;ZBTB16,non_coding_transcript_exon_variant,,ENST00000541602,,n.581C>A,MODIFIER,,,,1;ZBTB16,upstream_gene_variant,,ENST00000539918,,,MODIFIER,,,,1\tA\tENSG00000109906\tENST00000335953\tTranscript\tsynonymous_variant\tsynonymous_variant\t595/8494\t333/2022\t111/673\tI\tatC/atA\trs200027612;COSV100252118\t\t1\tZBTB16\tHGNC\tHGNC:12930\tprotein_coding\tYES\tCCDS8367.1\tENSP00000338157\tQ05516.216\tA0A024R3C6.52\tUPI000000018E\tQ05516-1\tNM_001354750.2;NM_006006.6;NM_001354751.2;NM_001354752.1\tNM_006006.6\tP1\t\t\t\t2/7\t\tPDB-ENSP_mappings:1buo.A;PDB-ENSP_mappings:1cs3.A;Low_complexity_(Seg):seg;CDD:cd18205;PANTHER:PTHR23226;PANTHER:PTHR23226:SF154;Gene3D:3.30.710.10;Pfam:PF00651;SMART:SM00225;Superfamily:SSF54695\t\t\t\t\t\t\t\t\t1.592e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0001307\t0.0001307\tgnomAD_SAS\t6.7599498834169935e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.00020824700186494738\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t0;1\t1\tGAGATCGAGTA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nOR10G8\t219869\tBI\tGRCh38\tchr11\t124029989\t124029989\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.367C>G\tp.Leu123Val\tp.L123V\tENST00000431524\t1/1\t139\t99\t39\t170\t\t\tOR10G8,missense_variant,p.L123V,ENST00000431524,NM_001004464.1,c.367C>G,MODERATE,YES,tolerated(0.8),benign(0.125),1;OR10G8,missense_variant,p.L123V,ENST00000641224,,c.367C>G,MODERATE,,tolerated(0.8),benign(0.125),1\tG\tENSG00000234560\tENST00000431524\tTranscript\tmissense_variant\tmissense_variant\t400/1045\t367/936\t123/311\tL/V\tCtg/Gtg\tCOSV101461811;COSV101461880;COSV70908305\t\t1\tOR10G8\tHGNC\tHGNC:14845\tprotein_coding\tYES\tCCDS31704.1\tENSP00000389072\tQ8NGN5.140\tA0A126GVX3.20\tUPI0000040A8F\t\tNM_001004464.1\t\tP1\t\ttolerated(0.8)\tbenign(0.125)\t1/1\t\tGene3D:1.20.1070.10;Pfam:PF13853;Prints:PR00237;PROSITE_profiles:PS50262;PANTHER:PTHR26453;PANTHER:PTHR26453:SF597;Superfamily:SSF81321;CDD:cd15916\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t\t\t1;1;1\t\tGCTACCTGGCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nVWF\t7450\tBI\tGRCh38\tchr12\t5996167\t5996167\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.5898C>T\tp.Phe1966=\tp.F1966=\tENST00000261405\t35/52\t37\t15\t22\t16\t\t\tVWF,synonymous_variant,p.F1966=,ENST00000261405,NM_000552.5,c.5898C>T,LOW,YES,,,-1;VWF,intron_variant,,ENST00000538635,,n.421-2233C>T,MODIFIER,,,,-1\tA\tENSG00000110799\tENST00000261405\tTranscript\tsynonymous_variant\tsynonymous_variant\t6148/8830\t5898/8442\t1966/2813\tF\tttC/ttT\tCOSV99780123\t\t-1\tVWF\tHGNC\tHGNC:12726\tprotein_coding\tYES\tCCDS8539.1\tENSP00000261405\tP04275.252\t\tUPI00001AE7EE\tP04275-1\tNM_000552.5\tNM_000552.5\tP1\t\t\t\t35/52\t\tPfam:PF00094;PIRSF:PIRSF002495;PROSITE_profiles:PS51233;PANTHER:PTHR11339;PANTHER:PTHR11339:SF361;SMART:SM00216\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t1\tAGCTTGAAATT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nUSP5\t8078\tBI\tGRCh38\tchr12\t6866036\t6866036\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2536G>A\tp.Asp846Asn\tp.D846N\tENST00000229268\t20/20\t119\t105\t14\t61\t\t\tUSP5,missense_variant,p.D846N,ENST00000229268,NM_001098536.2&NM_001382591.1&NM_001382588.1,c.2536G>A,MODERATE,YES,deleterious(0.04),probably_damaging(0.969),1;USP5,missense_variant,p.D823N,ENST00000389231,NM_001382590.1&NM_003481.3&NM_001382589.1,c.2467G>A,MODERATE,,deleterious(0.04),benign(0.367),1;TPI1,upstream_gene_variant,,ENST00000229270,,,MODIFIER,YES,,,1;TPI1,upstream_gene_variant,,ENST00000396705,NM_000365.6,,MODIFIER,,,,1;TPI1,upstream_gene_variant,,ENST00000462761,,,MODIFIER,,,,1;TPI1,upstream_gene_variant,,ENST00000488464,,,MODIFIER,,,,1;TPI1,upstream_gene_variant,,ENST00000493987,,,MODIFIER,,,,1;TPI1,upstream_gene_variant,,ENST00000495834,,,MODIFIER,,,,1;SPSB2,downstream_gene_variant,,ENST00000523102,NM_001146316.2&NM_001319670.2,,MODIFIER,,,,-1;SPSB2,downstream_gene_variant,,ENST00000524270,NM_032641.4,,MODIFIER,,,,-1;TPI1,upstream_gene_variant,,ENST00000535434,NM_001258026.1,,MODIFIER,,,,1;USP5,downstream_gene_variant,,ENST00000542087,,,MODIFIER,,,,1;TPI1,upstream_gene_variant,,ENST00000613953,NM_001159287.1,,MODIFIER,,,,1;USP5,downstream_gene_variant,,ENST00000541969,,,MODIFIER,,,,1;USP5,non_coding_transcript_exon_variant,,ENST00000537267,,n.1926G>A,MODIFIER,,,,1;USP5,non_coding_transcript_exon_variant,,ENST00000542371,,n.700G>A,MODIFIER,,,,1;TPI1,upstream_gene_variant,,ENST00000474253,,,MODIFIER,,,,1;TPI1,upstream_gene_variant,,ENST00000482209,,,MODIFIER,,,,1\tA\tENSG00000111667\tENST00000229268\tTranscript\tmissense_variant\tmissense_variant\t2566/3162\t2536/2577\t846/858\tD/N\tGac/Aac\tCOSV99979049\t\t1\tUSP5\tHGNC\tHGNC:12628\tprotein_coding\tYES\tCCDS41743.1\tENSP00000229268\tP45974.203\tA0A140VJZ1.30\tUPI00001379E1\tP45974-1\tNM_001098536.2;NM_001382591.1;NM_001382588.1\tNM_001098536.2\tA1\t\tdeleterious(0.04)\tprobably_damaging(0.969)\t20/20\t\tPDB-ENSP_mappings:3ihp.A;PDB-ENSP_mappings:3ihp.B;PROSITE_profiles:PS50235;CDD:cd02658;PANTHER:PTHR24006;PANTHER:PTHR24006:SF655;PIRSF:PIRSF016308;Pfam:PF00443;Superfamily:SSF54001\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCCAAGGACCTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nATN1\t1822\tBI\tGRCh38\tchr12\t6936884\t6936884\t+\tSilent\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1617G>C\tp.Leu539=\tp.L539=\tENST00000356654\t5/10\t221\t122\t99\t142\t\t\tATN1,synonymous_variant,p.L539=,ENST00000396684,NM_001940.4,c.1617G>C,LOW,YES,,,1;ATN1,synonymous_variant,p.L539=,ENST00000356654,NM_001007026.2,c.1617G>C,LOW,,,,1;ATN1,upstream_gene_variant,,ENST00000537488,,,MODIFIER,,,,1;ATN1,upstream_gene_variant,,ENST00000541029,,,MODIFIER,,,,1\tC\tENSG00000111676\tENST00000356654\tTranscript\tsynonymous_variant\tsynonymous_variant\t1854/4351\t1617/3573\t539/1190\tL\tctG/ctC\tCOSV100755958\t\t1\tATN1\tHGNC\tHGNC:3033\tprotein_coding\t\tCCDS31734.1\tENSP00000349076\tP54259.184\t\tUPI000006F554\t\tNM_001007026.2\t\tP1\t\t\t\t5/10\t\tPfam:PF03154;PANTHER:PTHR13859;PANTHER:PTHR13859:SF9;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t1\t1\tTCTCTGAGGCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPRB2\t653247\tBI\tGRCh38\tchr12\t11393117\t11393117\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.961C>G\tp.Pro321Ala\tp.P321A\tENST00000389362\t3/4\t1189\t745\t436\t698\t\t\tPRB2,missense_variant,p.P321A,ENST00000389362,NM_006248.4,c.961C>G,MODERATE,YES,tolerated_low_confidence(0.42),benign(0.102),-1;PRB1,intron_variant,,ENST00000546254,,c.100+1378C>G,MODIFIER,YES,,,-1;PRB2,downstream_gene_variant,,ENST00000565533,,,MODIFIER,,,,-1;PRB2,downstream_gene_variant,,ENST00000545829,,,MODIFIER,,,,-1\tC\tENSG00000121335\tENST00000389362\tTranscript\tmissense_variant\tmissense_variant\t999/1431\t961/1251\t321/416\tP/A\tCct/Gct\tCOSV101231500;COSV66983322\t\t-1\tPRB2\tHGNC\tHGNC:9338\tprotein_coding\tYES\tCCDS41757.2\tENSP00000374013\tP02812.138\t\tUPI0000EE5993\t\tNM_006248.4\tNM_006248.4\tP1\t\ttolerated_low_confidence(0.42)\tbenign(0.102)\t3/4\t\tPfam:PF15240;PANTHER:PTHR23203;PANTHER:PTHR23203:SF14;SMART:SM01412;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t5\t\t1;1\t\tTGGAGGAGGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;varscan2\nDDX23\t9416\tBI\tGRCh38\tchr12\t48831251\t48831251\t+\tSilent\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2130C>G\tp.Leu710=\tp.L710=\tENST00000308025\t16/17\t193\t142\t51\t158\t\t\tDDX23,synonymous_variant,p.L710=,ENST00000308025,NM_004818.3,c.2130C>G,LOW,YES,,,-1;DDX23,intron_variant,,ENST00000550834,,c.411-736C>G,MODIFIER,,,,-1;CACNB3,downstream_gene_variant,,ENST00000301050,NM_000725.4,,MODIFIER,YES,,,1;CACNB3,downstream_gene_variant,,ENST00000536187,NM_001206916.2,,MODIFIER,,,,1;CACNB3,downstream_gene_variant,,ENST00000540990,NM_001206917.2,,MODIFIER,,,,1;CACNB3,downstream_gene_variant,,ENST00000547230,NM_001206915.2,,MODIFIER,,,,1;CACNB3,downstream_gene_variant,,ENST00000547392,,,MODIFIER,,,,1;CACNB3,downstream_gene_variant,,ENST00000547818,,,MODIFIER,,,,1;CACNB3,downstream_gene_variant,,ENST00000550190,,,MODIFIER,,,,1;DDX23,non_coding_transcript_exon_variant,,ENST00000551331,,n.669C>G,MODIFIER,,,,-1;DDX23,downstream_gene_variant,,ENST00000547135,,,MODIFIER,,,,-1;DDX23,downstream_gene_variant,,ENST00000547165,,,MODIFIER,,,,-1;DDX23,downstream_gene_variant,,ENST00000547290,,,MODIFIER,,,,-1;DDX23,downstream_gene_variant,,ENST00000547842,,,MODIFIER,,,,-1;CACNB3,downstream_gene_variant,,ENST00000548860,,,MODIFIER,,,,1;DDX23,downstream_gene_variant,,ENST00000549795,,,MODIFIER,,,,-1;CACNB3,downstream_gene_variant,,ENST00000550483,,,MODIFIER,,,,1;CACNB3,downstream_gene_variant,,ENST00000551544,,,MODIFIER,,,,1;CACNB3,downstream_gene_variant,,ENST00000552480,,,MODIFIER,,,,1;DDX23,downstream_gene_variant,,ENST00000552802,,,MODIFIER,,,,-1;DDX23,downstream_gene_variant,,ENST00000553065,,,MODIFIER,,,,-1\tC\tENSG00000174243\tENST00000308025\tTranscript\tsynonymous_variant\tsynonymous_variant\t2210/3256\t2130/2463\t710/820\tL\tctC/ctG\tCOSV99975098\t\t-1\tDDX23\tHGNC\tHGNC:17347\tprotein_coding\tYES\tCCDS8770.1\tENSP00000310723\tQ9BUQ8.181\tA0A024R0Z3.44\tUPI0000073875\tQ9BUQ8-1\tNM_004818.3\tNM_004818.3\tP1\t\t\t\t16/17\t\tPDB-ENSP_mappings:3jcr.F;PDB-ENSP_mappings:4nho.A;PDB-ENSP_mappings:6ah0.X;PDB-ENSP_mappings:6qw6.5X;PDB-ENSP_mappings:6qx9.5X;PROSITE_profiles:PS51194;CDD:cd18787;PANTHER:PTHR11824:SF8;PANTHER:PTHR11824;Pfam:PF00271;Gene3D:3.40.50.300;SMART:SM00490;Superfamily:SSF52540\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t1\tGCCTTGAGGTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nKMT2D\t8085\tBI\tGRCh38\tchr12\t49026491\t49026491\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.15475C>T\tp.Arg5159Trp\tp.R5159W\tENST00000301067\t49/55\t72\t48\t24\t65\t\t\tKMT2D,missense_variant,p.R5159W,ENST00000301067,NM_003482.4,c.15475C>T,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;KMT2D,upstream_gene_variant,,ENST00000526209,,,MODIFIER,,,,-1;KMT2D,downstream_gene_variant,,ENST00000552391,,,MODIFIER,,,,-1\tA\tENSG00000167548\tENST00000301067\tTranscript\tmissense_variant\tmissense_variant\t16694/20635\t15475/16614\t5159/5537\tR/W\tCgg/Tgg\tCOSV99985687\t\t-1\tKMT2D\tHGNC\tHGNC:7133\tprotein_coding\tYES\tCCDS44873.1\tENSP00000301067\tO14686.191\t\tUPI0000EE84D6\tO14686-1\tNM_003482.4\tNM_003482.4\tP1\t\tdeleterious(0)\tprobably_damaging(0.999)\t49/55\t\tPANTHER:PTHR45888;PANTHER:PTHR45888:SF2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t5\t\t1\t1\tGTCCCGCTCAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCSRNP2\t81566\tBI\tGRCh38\tchr12\t51073913\t51073913\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.321C>T\tp.Leu107=\tp.L107=\tENST00000228515\t3/5\t109\t71\t38\t123\t\t\tCSRNP2,synonymous_variant,p.L107=,ENST00000228515,NM_030809.3,c.321C>T,LOW,YES,,,-1;CSRNP2,synonymous_variant,p.L107=,ENST00000548981,,c.321C>T,LOW,,,,-1;CSRNP2,synonymous_variant,p.L13=,ENST00000548206,,c.39C>T,LOW,,,,-1;CSRNP2,downstream_gene_variant,,ENST00000546935,,,MODIFIER,,,,-1;CSRNP2,downstream_gene_variant,,ENST00000552899,,,MODIFIER,,,,-1;CSRNP2,downstream_gene_variant,,ENST00000550461,,,MODIFIER,,,,-1;CSRNP2,downstream_gene_variant,,ENST00000552680,,,MODIFIER,,,,-1;CSRNP2,downstream_gene_variant,,ENST00000550533,,,MODIFIER,,,,-1\tA\tENSG00000110925\tENST00000228515\tTranscript\tsynonymous_variant\tsynonymous_variant\t665/4517\t321/1632\t107/543\tL\tctC/ctT\tCOSV99950505\t\t-1\tCSRNP2\tHGNC\tHGNC:16006\tprotein_coding\tYES\tCCDS8807.1\tENSP00000228515\tQ9H175.133\t\tUPI0000073111\t\tNM_030809.3\tNM_030809.3\tP1\t\t\t\t3/5\t\tPANTHER:PTHR13580:SF6;PANTHER:PTHR13580;Pfam:PF16019\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tTCACAGAGTGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTAFA2\t338811\tBI\tGRCh38\tchr12\t61867400\t61867400\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs1240873111\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.26C>T\tp.Ala9Val\tp.A9V\tENST00000416284\t2/5\t47\t34\t13\t41\t\t\tTAFA2,missense_variant,p.A9V,ENST00000416284,NM_178539.4,c.26C>T,MODERATE,YES,tolerated_low_confidence(0.53),benign(0),-1;TAFA2,missense_variant,p.A9V,ENST00000551619,,c.26C>T,MODERATE,,tolerated_low_confidence(0.53),benign(0),-1;TAFA2,missense_variant,p.A9V,ENST00000551449,,c.26C>T,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.682),-1;TAFA2,missense_variant,p.A10V,ENST00000552075,,c.29C>T,MODERATE,,tolerated_low_confidence(0.55),benign(0.005),-1;TAFA2,missense_variant,p.A10V,ENST00000548780,,c.29C>T,MODERATE,,tolerated(0.55),possibly_damaging(0.682),-1;TAFA2,missense_variant,p.A16V,ENST00000549958,,c.47C>T,MODERATE,,tolerated(0.58),benign(0.003),-1;TAFA2,missense_variant,p.A9V,ENST00000549379,,c.26C>T,MODERATE,,tolerated_low_confidence(0.55),benign(0.007),-1\tA\tENSG00000198673\tENST00000416284\tTranscript\tmissense_variant\tmissense_variant\t1611/4128\t26/396\t9/131\tA/V\tgCa/gTa\trs1240873111;COSV101353931\t\t-1\tTAFA2\tHGNC\tHGNC:21589\tprotein_coding\tYES\tCCDS8962.1\tENSP00000393987\tQ8N3H0.114\t\tUPI000006F642\tQ8N3H0-1\tNM_178539.4\t\tP1\t\ttolerated_low_confidence(0.53)\tbenign(0)\t2/5\t\tPANTHER:PTHR31770:SF1;PANTHER:PTHR31770\t\t\t\t\t\t\t\t\t4.009e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t3.298e-05\t3.298e-05\tgnomAD_SAS\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t0;1\t\tTTGTTGCTTTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nLRRIQ1\t84125\tBI\tGRCh38\tchr12\t85056506\t85056506\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1713G>A\tp.Glu571=\tp.E571=\tENST00000393217\t8/27\t19\t13\t5\t27\t\t\tLRRIQ1,synonymous_variant,p.E571=,ENST00000393217,NM_001079910.2,c.1713G>A,LOW,YES,,,1;LRRIQ1,downstream_gene_variant,,ENST00000533414,,,MODIFIER,,,,1;LRRIQ1,non_coding_transcript_exon_variant,,ENST00000525971,,n.1831G>A,MODIFIER,,,,1\tA\tENSG00000133640\tENST00000393217\tTranscript\tsynonymous_variant\tsynonymous_variant\t1794/5414\t1713/5169\t571/1722\tE\tgaG/gaA\tCOSV101280707\t\t1\tLRRIQ1\tHGNC\tHGNC:25708\tprotein_coding\tYES\tCCDS41816.1\tENSP00000376910\tQ96JM4.122\tA0A140VJN5.22\tUPI0000ED4E82\tQ96JM4-4\tNM_001079910.2\tNM_001079910.2\tP1\t\t\t\t8/27\t\tCoiled-coils_(Ncoils):Coil;PANTHER:PTHR10877;PANTHER:PTHR10877:SF184\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tGAAGAGCAGAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPOC1B-GALNT4\t100528030\tBI\tGRCh38\tchr12\t89523991\t89523991\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.550G>C\tp.Glu184Gln\tp.E184Q\tENST00000548729\t3/3\t66\t45\t21\t70\t\t\tPOC1B-GALNT4,missense_variant,p.E184Q,ENST00000548729,NM_001199782.1&NM_001199781.2,c.550G>C,MODERATE,YES,deleterious(0.01),benign(0.335),-1;GALNT4,missense_variant,p.E187Q,ENST00000529983,NM_003774.5,c.559G>C,MODERATE,YES,deleterious(0.04),possibly_damaging(0.466),-1;POC1B,intron_variant,,ENST00000313546,NM_172240.3,c.100+1129G>C,MODIFIER,YES,,,-1;POC1B,intron_variant,,ENST00000393179,,c.-119+1129G>C,MODIFIER,,,,-1;POC1B-GALNT4,intron_variant,,ENST00000547474,,c.101-318G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000549035,NM_001199777.2,c.-27+1129G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000549504,,c.-119+1129G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000539190,,n.198+1129G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000546830,,c.100+1129G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000547274,,c.100+1129G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000547496,,c.100+1129G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000548715,,c.100+1129G>C,MODIFIER,,,,-1;POC1B,intron_variant,,ENST00000552563,,n.296+1129G>C,MODIFIER,,,,-1;POC1B-AS1,upstream_gene_variant,,ENST00000605233,,,MODIFIER,YES,,,1;POC1B-AS1,upstream_gene_variant,,ENST00000655646,,,MODIFIER,,,,1\tG\tENSG00000259075\tENST00000548729\tTranscript\tmissense_variant\tmissense_variant\t853/5436\t550/1728\t184/575\tE/Q\tGaa/Caa\tCOSV100544517\t\t-1\tPOC1B-GALNT4\tHGNC\tHGNC:42957\tprotein_coding\tYES\t\tENSP00000447852\t\tF8VUJ3.66\tUPI0000228FE1\t\tNM_001199782.1;NM_001199781.2\t\tP1\t\tdeleterious(0.01)\tbenign(0.335)\t3/3\t\tCDD:cd02510;PANTHER:PTHR11675;PANTHER:PTHR11675:SF7;Pfam:PF00535;Gene3D:3.90.550.10;Superfamily:SSF53448\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t2\t\t1\t\tAGTTTCAAGTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPARPBP\t55010\tBI\tGRCh38\tchr12\t102148332\t102148332\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.256G>A\tp.Asp86Asn\tp.D86N\tENST00000327680\t3/11\t67\t54\t13\t56\t\t\tPARPBP,missense_variant,p.D86N,ENST00000327680,NM_017915.5&NM_001382725.1&NM_001382723.1&NM_001382724.1&NM_001382721.1&NM_001382722.1&NM_001382726.1,c.256G>A,MODERATE,,tolerated(0.05),benign(0.295),1;PARPBP,missense_variant,p.D86N,ENST00000541394,NM_001319988.2,c.256G>A,MODERATE,YES,tolerated(0.06),benign(0.198),1;PARPBP,missense_variant,p.D53N,ENST00000417507,NM_001382729.1&NM_001382731.1,c.157G>A,MODERATE,,deleterious(0.04),benign(0.093),1;PARPBP,missense_variant,p.D53N,ENST00000412715,NM_001382732.1,c.157G>A,MODERATE,,deleterious(0.04),benign(0.372),1;PARPBP,missense_variant,p.D5N,ENST00000392911,NM_001319993.2&NM_001319994.2&NM_001382728.1,c.13G>A,MODERATE,,tolerated(0.07),benign(0.295),1;PARPBP,missense_variant,p.D86N,ENST00000537257,NM_001319996.2,c.256G>A,MODERATE,,deleterious(0.04),benign(0.295),1;PARPBP,intron_variant,,ENST00000543784,NM_001382735.1,c.154-16106G>A,MODIFIER,,,,1;PARPBP,non_coding_transcript_exon_variant,,ENST00000541668,,n.368G>A,MODIFIER,,,,1;PARPBP,intron_variant,,ENST00000535811,,n.54+24291G>A,MODIFIER,,,,1;PARPBP,missense_variant,p.D86N,ENST00000392909,,c.256G>A,MODERATE,,deleterious(0.04),benign(0.085),1;PARPBP,non_coding_transcript_exon_variant,,ENST00000392914,,n.259G>A,MODIFIER,,,,1;PARPBP,intron_variant,,ENST00000457614,,c.55-5537G>A,MODIFIER,,,,1\tA\tENSG00000185480\tENST00000327680\tTranscript\tmissense_variant\tmissense_variant\t363/3076\t256/1740\t86/579\tD/N\tGac/Aac\tCOSV100569312\t\t1\tPARPBP\tHGNC\tHGNC:26074\tprotein_coding\t\tCCDS9090.2\tENSP00000332915\tQ9NWS1.121\t\tUPI000004A06B\tQ9NWS1-1\tNM_017915.5;NM_001382725.1;NM_001382723.1;NM_001382724.1;NM_001382721.1;NM_001382722.1;NM_001382726.1\tNM_017915.5\tP4\t\ttolerated(0.05)\tbenign(0.295)\t3/11\t\tPANTHER:PTHR32121\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t2\t\t1\t\tTGACTGACCAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nRPLP0\t6175\tBI\tGRCh38\tchr12\t120199142\t120199142\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.294C>T\tp.Ile98=\tp.I98=\tENST00000228306\t4/8\t76\t64\t12\t62\t\t\tRPLP0,synonymous_variant,p.I98=,ENST00000551150,,c.294C>T,LOW,YES,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000228306,NM_053275.3,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000392514,NM_001002.4,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000550856,,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000546989,,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000313104,,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I78=,ENST00000547211,,c.234C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000546990,,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I84=,ENST00000547191,,c.252C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I84=,ENST00000550423,,c.252C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000551914,,c.294C>T,LOW,,,,-1;GCN1,upstream_gene_variant,,ENST00000300648,NM_006836.2,,MODIFIER,YES,,,-1;RPLP0,upstream_gene_variant,,ENST00000552292,,,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000550296,,n.336C>T,MODIFIER,,,,-1;RPLP0,downstream_gene_variant,,ENST00000551336,,,MODIFIER,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000551258,,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000547173,,c.294C>T,LOW,,,,-1;RPLP0,synonymous_variant,p.I98=,ENST00000547475,,c.294C>T,LOW,,,,-1;RPLP0,3_prime_UTR_variant,,ENST00000549098,,c.*131C>T,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000552461,,n.1865C>T,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000548568,,n.343C>T,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000552902,,n.600C>T,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000546564,,n.375C>T,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000548495,,n.485C>T,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000548551,,n.381C>T,MODIFIER,,,,-1;RPLP0,non_coding_transcript_exon_variant,,ENST00000549242,,n.474C>T,MODIFIER,,,,-1;RPLP0,upstream_gene_variant,,ENST00000551217,,,MODIFIER,,,,-1;RPLP0,downstream_gene_variant,,ENST00000551783,,,MODIFIER,,,,-1;PXN-AS1,upstream_gene_variant,,ENST00000535200,,,MODIFIER,,,,1;PXN-AS1,upstream_gene_variant,,ENST00000538804,,,MODIFIER,,,,1;PXN-AS1,upstream_gene_variant,,ENST00000539446,,,MODIFIER,,,,1;PXN-AS1,upstream_gene_variant,,ENST00000542265,,,MODIFIER,,,,1;PXN-AS1,upstream_gene_variant,,ENST00000542314,,,MODIFIER,,,,1;PXN-AS1,upstream_gene_variant,,ENST00000664264,,,MODIFIER,,,,1;PXN-AS1,upstream_gene_variant,,ENST00000667017,,,MODIFIER,YES,,,1;PXN-AS1,upstream_gene_variant,,ENST00000667721,,,MODIFIER,,,,1\tA\tENSG00000089157\tENST00000228306\tTranscript\tsynonymous_variant\tsynonymous_variant\t531/1257\t294/954\t98/317\tI\tatC/atT\tCOSV99935468\t\t-1\tRPLP0\tHGNC\tHGNC:10371\tprotein_coding\t\tCCDS9193.1\tENSP00000339027\tP05388.222\tA0A024RBS2.51\tUPI0000134221\tP05388-1\tNM_053275.3\t\tP1\t\t\t\t4/8\t\tPDB-ENSP_mappings:4v6w.Cq;PDB-ENSP_mappings:4v6x.Cq;PDB-ENSP_mappings:5aj0.AK;PDB-ENSP_mappings:6olg.AK;CDD:cd05795;PANTHER:PTHR45699:SF1;PANTHER:PTHR45699;Gene3D:3.30.70.1730;PIRSF:PIRSF039087;Pfam:PF00466;Superfamily:SSF160369\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t1\t\tTCCCTGATCTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nKNTC1\t9735\tBI\tGRCh38\tchr12\t122569728\t122569728\t+\tSilent\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1764C>G\tp.Leu588=\tp.L588=\tENST00000333479\t22/64\t65\t46\t19\t55\t\t\tKNTC1,synonymous_variant,p.L588=,ENST00000333479,NM_014708.6,c.1764C>G,LOW,YES,,,1;KNTC1,synonymous_variant,p.L551=,ENST00000450485,,c.1653C>G,LOW,,,,1\tG\tENSG00000184445\tENST00000333479\tTranscript\tsynonymous_variant\tsynonymous_variant\t1940/6974\t1764/6630\t588/2209\tL\tctC/ctG\tCOSV100338806\t\t1\tKNTC1\tHGNC\tHGNC:17255\tprotein_coding\tYES\tCCDS45002.1\tENSP00000328236\tP50748.163\t\tUPI0000047FD6\tP50748-1\tNM_014708.6\tNM_014708.6\tP1\t\t\t\t22/64\t\tPANTHER:PTHR15688;Pfam:PF10493\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tTTGCTCAACTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nRFLNA\t144347\tBI\tGRCh38\tchr12\t124311895\t124311895\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.285C>T\tp.Ile95=\tp.I95=\tENST00000546355\t2/3\t38\t26\t12\t25\t\t\tRFLNA,synonymous_variant,p.I95=,ENST00000546355,NM_001365156.1,c.285C>T,LOW,YES,,,1;RFLNA,synonymous_variant,p.I14=,ENST00000389727,NM_001204299.3&NM_001347902.2,c.42C>T,LOW,,,,1;RFLNA,synonymous_variant,p.I14=,ENST00000324038,NM_181709.4,c.42C>T,LOW,,,,1;RFLNA,synonymous_variant,p.I14=,ENST00000338359,,c.42C>T,LOW,,,,1\tT\tENSG00000178882\tENST00000546355\tTranscript\tsynonymous_variant\tsynonymous_variant\t622/2487\t285/651\t95/216\tI\tatC/atT\tCOSV100133432\t\t1\tRFLNA\tHGNC\tHGNC:27051\tprotein_coding\tYES\t\tENSP00000444080\tQ6ZTI6.104\t\tUPI000022912B\tQ6ZTI6-1\tNM_001365156.1\tNM_001365156.1\tP1\t\t\t\t2/3\t\tPANTHER:PTHR31848:SF0;PANTHER:PTHR31848;Pfam:PF15068\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tAGCATCAAGGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nATP12A\t479\tBI\tGRCh38\tchr13\t24709397\t24709397\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs781024371\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2527G>A\tp.Glu843Lys\tp.E843K\tENST00000381946\t18/23\t55\t32\t23\t75\t\t\tATP12A,missense_variant,p.E843K,ENST00000381946,NM_001676.7,c.2527G>A,MODERATE,,deleterious(0.02),probably_damaging(0.998),1;ATP12A,missense_variant,p.E849K,ENST00000218548,NM_001185085.1,c.2545G>A,MODERATE,YES,deleterious(0.02),probably_damaging(0.946),1;RPL26P34,upstream_gene_variant,,ENST00000431005,,,MODIFIER,YES,,,-1\tA\tENSG00000075673\tENST00000381946\tTranscript\tmissense_variant\tmissense_variant\t2863/4406\t2527/3120\t843/1039\tE/K\tGaa/Aaa\trs781024371;COSV99518463\t\t1\tATP12A\tHGNC\tHGNC:13816\tprotein_coding\t\tCCDS31948.1\tENSP00000371372\tP54707.198\t\tUPI000016B154\tP54707-1\tNM_001676.7\tNM_001676.7\tP1\t\tdeleterious(0.02)\tprobably_damaging(0.998)\t18/23\t\tGene3D:1.20.1110.10;Pfam:PF00689;PANTHER:PTHR43294;PANTHER:PTHR43294:SF1;Superfamily:SSF81665;TIGRFAM:TIGR01106;CDD:cd02608\t\t\t\t\t\t\t\t\t3.978e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.79e-06\t0.0\t0.0\t8.79e-06\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t0;1\t\tAAGCTGAAAGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nKPNA3\t3839\tBI\tGRCh38\tchr13\t49722527\t49722527\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.506C>T\tp.Pro169Leu\tp.P169L\tENST00000261667\t8/17\t41\t15\t26\t30\t\t\tKPNA3,missense_variant,p.P169L,ENST00000261667,NM_002267.4,c.506C>T,MODERATE,YES,deleterious(0.03),benign(0.019),-1\tA\tENSG00000102753\tENST00000261667\tTranscript\tmissense_variant\tmissense_variant\t682/4222\t506/1566\t169/521\tP/L\tcCa/cTa\tCOSV99904365\t\t-1\tKPNA3\tHGNC\tHGNC:6396\tprotein_coding\tYES\tCCDS9421.1\tENSP00000261667\tO00505.203\tA0A024RDV7.36\tUPI000012D5F9\t\tNM_002267.4\tNM_002267.4\tP1\t\tdeleterious(0.03)\tbenign(0.019)\t8/17\t\tGene3D:1.25.10.10;Pfam:PF00514;PIRSF:PIRSF005673;PROSITE_profiles:PS50176;PANTHER:PTHR23316;PANTHER:PTHR23316:SF6;SMART:SM00185;Superfamily:SSF48371\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t6.766720161976991e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.5439200069522485e-05\t0.0\t0.0\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tGATGTGGTGAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nVPS36\t51028\tBI\tGRCh38\tchr13\t52436292\t52436292\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.349G>C\tp.Glu117Gln\tp.E117Q\tENST00000378060\t4/14\t15\t10\t5\t15\t\t\tVPS36,missense_variant,p.E59Q,ENST00000611132,NM_001282169.1,c.175G>C,MODERATE,,tolerated(0.14),benign(0.109),-1;VPS36,missense_variant,p.E117Q,ENST00000378060,NM_001282168.2&NM_016075.4,c.349G>C,MODERATE,YES,tolerated(0.12),benign(0.109),-1;VPS36,splice_region_variant,,ENST00000480923,,n.567G>C,LOW,,,,-1;VPS36,missense_variant,p.E117Q,ENST00000650274,,c.349G>C,MODERATE,,tolerated(0.12),benign(0.287),-1;VPS36,non_coding_transcript_exon_variant,,ENST00000475375,,n.383G>C,MODIFIER,,,,-1\tG\tENSG00000136100\tENST00000378060\tTranscript\tmissense_variant\tmissense_variant;splice_region_variant\t389/4425\t349/1161\t117/386\tE/Q\tGag/Cag\tCOSV100955294\t\t-1\tVPS36\tHGNC\tHGNC:20312\tprotein_coding\tYES\tCCDS9434.1\tENSP00000367299\tQ86VN1.159\t\tUPI000013CFE6\tQ86VN1-1\tNM_001282168.2;NM_016075.4\tNM_016075.4\tP1\t\ttolerated(0.12)\tbenign(0.109)\t4/14\t\tPDB-ENSP_mappings:2hth.B;PROSITE_profiles:PS51495;CDD:cd13226;PANTHER:PTHR13128;Gene3D:2.30.29.30;Superfamily:SSF50729\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tTACCTCAATCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nPCDH9\t5101\tBI\tGRCh38\tchr13\t66304936\t66304936\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.3433C>T\tp.Pro1145Ser\tp.P1145S\tENST00000377865\t5/5\t115\t28\t87\t121\t\t\tPCDH9,missense_variant,p.P1111S,ENST00000544246,NM_001318373.2&NM_020403.5,c.3331C>T,MODERATE,,deleterious(0),possibly_damaging(0.496),-1;PCDH9,missense_variant,p.P1145S,ENST00000377865,NM_203487.3,c.3433C>T,MODERATE,YES,deleterious(0),benign(0.373),-1;PCDH9,missense_variant,p.P1103S,ENST00000456367,NM_001318372.2,c.3307C>T,MODERATE,,deleterious(0),benign(0.373),-1;PCDH9,non_coding_transcript_exon_variant,,ENST00000617020,,n.227C>T,MODIFIER,,,,-1;PCDH9,downstream_gene_variant,,ENST00000614931,,,MODIFIER,,,,-1;PCDH9-AS1,intron_variant,,ENST00000430861,,n.144+922G>A,MODIFIER,YES,,,1\tA\tENSG00000184226\tENST00000377865\tTranscript\tmissense_variant\tmissense_variant\t4125/6227\t3433/3714\t1145/1237\tP/S\tCct/Tct\tCOSV60592024\t\t-1\tPCDH9\tHGNC\tHGNC:8661\tprotein_coding\tYES\tCCDS9444.1\tENSP00000367096\tQ9HC56.155\tX5D7N0.40\tUPI00001FCE90\tQ9HC56-1\tNM_203487.3\tNM_203487.3\tA1\t\tdeleterious(0)\tbenign(0.373)\t5/5\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tAGGAGGCATCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM75863\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nBORA\t79866\tBI\tGRCh38\tchr13\t72731297\t72731297\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.395G>C\tp.Arg132Thr\tp.R132T\tENST00000613797\t3/12\t130\t112\t18\t44\t\t\tBORA,missense_variant,p.R132T,ENST00000613797,,c.395G>C,MODERATE,YES,deleterious(0.04),possibly_damaging(0.844),1;BORA,missense_variant,p.R57T,ENST00000390667,NM_001286746.3&NM_024808.5,c.170G>C,MODERATE,,tolerated(0.11),possibly_damaging(0.876),1;BORA,missense_variant,p.R57T,ENST00000651477,,c.170G>C,MODERATE,,tolerated(0.11),possibly_damaging(0.876),1;BORA,missense_variant,p.R35T,ENST00000377814,,c.104G>C,MODERATE,,tolerated(0.11),possibly_damaging(0.457),1;BORA,intron_variant,,ENST00000652266,NM_001286747.1&NM_001366664.2,c.50+2204G>C,MODIFIER,,,,1;MZT1,upstream_gene_variant,,ENST00000377818,NM_001071775.3,,MODIFIER,YES,,,-1;BORA,non_coding_transcript_exon_variant,,ENST00000464754,,n.265G>C,MODIFIER,,,,1;BORA,intron_variant,,ENST00000471712,,n.251+2204G>C,MODIFIER,,,,1;BORA,intron_variant,,ENST00000618209,,c.153+2204G>C,MODIFIER,,,,1;BORA,intron_variant,,ENST00000651376,,c.153+2204G>C,MODIFIER,,,,1\tC\tENSG00000136122\tENST00000613797\tTranscript\tmissense_variant\tmissense_variant\t542/3034\t395/1905\t132/634\tR/T\taGa/aCa\tCOSV100909754\t\t1\tBORA\tHGNC\tHGNC:24724\tprotein_coding\tYES\tCCDS73583.1\tENSP00000479266\t\tA0A087WV86.42\tUPI0003C41951\t\t\t\tA2\t\tdeleterious(0.04)\tpossibly_damaging(0.844)\t3/12\t\tPfam:PF15280;Prints:PR02038;PANTHER:PTHR14728\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tATTTAGATGGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nMYCBP2\t23077\tBI\tGRCh38\tchr13\t77191790\t77191790\t+\tMissense_Mutation\tSNP\tT\tT\tC\trs987490418\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.3845A>G\tp.Asp1282Gly\tp.D1282G\tENST00000357337\t29/84\t75\t26\t49\t29\t\t\tMYCBP2,missense_variant,p.D1320G,ENST00000544440,NM_015057.5,c.3959A>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.995),-1;MYCBP2,missense_variant,p.D1282G,ENST00000357337,,c.3845A>G,MODERATE,,deleterious(0.01),probably_damaging(0.919),-1\tC\tENSG00000005810\tENST00000357337\tTranscript\tmissense_variant\tmissense_variant\t3938/14736\t3845/13923\t1282/4640\tD/G\tgAt/gGt\trs987490418;COSV100631838\t\t-1\tMYCBP2\tHGNC\tHGNC:23386\tprotein_coding\t\t\tENSP00000349892\t\tA0A499FJI4.5\tUPI0000212757\t\t\t\tA2\t\tdeleterious(0.01)\tprobably_damaging(0.919)\t29/84\t\tGene3D:2.60.120.820;Pfam:PF08005;PANTHER:PTHR45943;PANTHER:PTHR45943:SF1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t0;1\t\tGCTCATCAAAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nUBAC2\t337867\tBI\tGRCh38\tchr13\t99385334\t99385334\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1034G>A\tp.Ter345=\tp.*345=\tENST00000403766\t9/9\t57\t30\t27\t36\t\t\tUBAC2,stop_retained_variant,p.*310=,ENST00000376440,NM_177967.4,c.929G>A,LOW,,,,1;UBAC2,stop_retained_variant,p.*345=,ENST00000403766,NM_001144072.2,c.1034G>A,LOW,YES,,,1;UBAC2,downstream_gene_variant,,ENST00000355700,,,MODIFIER,,,,1;UBAC2,non_coding_transcript_exon_variant,,ENST00000460562,,n.1250G>A,MODIFIER,,,,1;UBAC2,non_coding_transcript_exon_variant,,ENST00000494576,,n.755G>A,MODIFIER,,,,1;UBAC2,non_coding_transcript_exon_variant,,ENST00000480738,,n.653G>A,MODIFIER,,,,1;UBAC2,non_coding_transcript_exon_variant,,ENST00000473194,,n.801G>A,MODIFIER,,,,1\tA\tENSG00000134882\tENST00000403766\tTranscript\tstop_retained_variant\tstop_retained_variant\t1089/2259\t1034/1035\t345/344\t*\ttGa/tAa\tCOSV100854080\t\t1\tUBAC2\tHGNC\tHGNC:20486\tprotein_coding\tYES\tCCDS45064.1\tENSP00000383911\tQ8NBM4.149\tA0A024RE02.45\tUPI000003B0B4\tQ8NBM4-1\tNM_001144072.2\tNM_001144072.2\tP1\t\t\t\t9/9\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t2\t\t1\t1\tGCACTGATAGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNALCN\t259232\tBI\tGRCh38\tchr13\t101292256\t101292256\t+\tMissense_Mutation\tSNP\tT\tT\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.910A>G\tp.Thr304Ala\tp.T304A\tENST00000251127\t8/44\t49\t28\t21\t45\t\t\tNALCN,missense_variant,p.T304A,ENST00000251127,NM_001350749.2&NM_052867.4,c.910A>G,MODERATE,,deleterious(0.01),possibly_damaging(0.53),-1;NALCN,missense_variant,p.T304A,ENST00000675332,NM_001350748.2,c.910A>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.922),-1;NALCN,missense_variant,p.T304A,ENST00000676315,NM_001350751.2&NM_001350750.2,c.910A>G,MODERATE,,tolerated(0.07),possibly_damaging(0.875),-1;NALCN,missense_variant,p.T304A,ENST00000675150,,c.910A>G,MODERATE,,tolerated(0.09),possibly_damaging(0.901),-1;NALCN,missense_variant,p.T304A,ENST00000675802,,c.910A>G,MODERATE,,deleterious(0),probably_damaging(0.98),-1;NALCN,non_coding_transcript_exon_variant,,ENST00000676439,,n.1084A>G,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,,n.1006A>G,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000675415,,n.1093A>G,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000674840,,n.1008A>G,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000674904,,n.990A>G,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000675075,,n.512A>G,MODIFIER,,,,-1;NALCN,missense_variant,p.T304A,ENST00000648359,,c.910A>G,MODERATE,,tolerated(0.07),possibly_damaging(0.771),-1;NALCN,3_prime_UTR_variant,,ENST00000675594,,c.*347A>G,MODIFIER,,,,-1;NALCN,3_prime_UTR_variant,,ENST00000497170,,c.*104A>G,MODIFIER,,,,-1\tC\tENSG00000102452\tENST00000251127\tTranscript\tmissense_variant\tmissense_variant\t1145/6971\t910/5217\t304/1738\tT/A\tAct/Gct\tCOSV51933681\t\t-1\tNALCN\tHGNC\tHGNC:19082\tprotein_coding\t\tCCDS9498.1\tENSP00000251127\tQ8IZF0.168\tA0A024RE05.44\tUPI000004EBBD\tQ8IZF0-1\tNM_001350749.2;NM_052867.4\tNM_052867.4\tP1\t\tdeleterious(0.01)\tpossibly_damaging(0.53)\t8/44\t\tGene3D:1.10.287.70;Pfam:PF00520;PANTHER:PTHR46141;PANTHER:PTHR46141:SF1;Superfamily:SSF81324;Transmembrane_helices:TMhelix\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t1\tGAGAGTGATGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM5965127;COSM5965128\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNALCN\t259232\tBI\tGRCh38\tchr13\t101292257\t101292257\t+\tSilent\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.909C>A\tp.Ile303=\tp.I303=\tENST00000251127\t8/44\t50\t29\t20\t44\t\t\tNALCN,synonymous_variant,p.I303=,ENST00000251127,NM_001350749.2&NM_052867.4,c.909C>A,LOW,,,,-1;NALCN,synonymous_variant,p.I303=,ENST00000675332,NM_001350748.2,c.909C>A,LOW,YES,,,-1;NALCN,synonymous_variant,p.I303=,ENST00000676315,NM_001350751.2&NM_001350750.2,c.909C>A,LOW,,,,-1;NALCN,synonymous_variant,p.I303=,ENST00000675150,,c.909C>A,LOW,,,,-1;NALCN,synonymous_variant,p.I303=,ENST00000675802,,c.909C>A,LOW,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000676439,,n.1083C>A,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000470333,,n.1005C>A,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000675415,,n.1092C>A,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000674840,,n.1007C>A,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000674904,,n.989C>A,MODIFIER,,,,-1;NALCN,non_coding_transcript_exon_variant,,ENST00000675075,,n.511C>A,MODIFIER,,,,-1;NALCN,synonymous_variant,p.I303=,ENST00000648359,,c.909C>A,LOW,,,,-1;NALCN,3_prime_UTR_variant,,ENST00000675594,,c.*346C>A,MODIFIER,,,,-1;NALCN,3_prime_UTR_variant,,ENST00000497170,,c.*103C>A,MODIFIER,,,,-1\tT\tENSG00000102452\tENST00000251127\tTranscript\tsynonymous_variant\tsynonymous_variant\t1144/6971\t909/5217\t303/1738\tI\tatC/atA\tCOSV99217665\t\t-1\tNALCN\tHGNC\tHGNC:19082\tprotein_coding\t\tCCDS9498.1\tENSP00000251127\tQ8IZF0.168\tA0A024RE05.44\tUPI000004EBBD\tQ8IZF0-1\tNM_001350749.2;NM_052867.4\tNM_052867.4\tP1\t\t\t\t8/44\t\tGene3D:1.10.287.70;Pfam:PF00520;PANTHER:PTHR46141;PANTHER:PTHR46141:SF1;Superfamily:SSF81324;Transmembrane_helices:TMhelix\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t1\t1\tAGAGTGATGAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nITGBL1\t9358\tBI\tGRCh38\tchr13\t101575495\t101575495\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.535G>A\tp.Glu179Lys\tp.E179K\tENST00000376180\t4/11\t198\t158\t40\t205\t\t\tITGBL1,missense_variant,p.E38K,ENST00000545560,NM_001271754.2,c.112G>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;ITGBL1,missense_variant,p.E179K,ENST00000376180,NM_004791.3,c.535G>A,MODERATE,YES,deleterious(0.03),probably_damaging(0.998),1;ITGBL1,missense_variant,p.E86K,ENST00000622834,,c.256G>A,MODERATE,,deleterious(0),probably_damaging(0.994),1;ITGBL1,missense_variant,p.E130K,ENST00000618057,NM_001271755.1,c.388G>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;ITGBL1,missense_variant,p.E86K,ENST00000376162,NM_001271756.1,c.256G>A,MODERATE,,deleterious(0),probably_damaging(0.993),1\tA\tENSG00000198542\tENST00000376180\tTranscript\tmissense_variant\tmissense_variant\t694/2436\t535/1485\t179/494\tE/K\tGag/Aag\tCOSV101095723\t\t1\tITGBL1\tHGNC\tHGNC:6164\tprotein_coding\tYES\tCCDS9499.1\tENSP00000365351\tO95965.171\tA0A024RDW7.36\tUPI0000073C95\tO95965-1\tNM_004791.3\tNM_004791.3\tP1\t\tdeleterious(0.03)\tprobably_damaging(0.998)\t4/11\t\tGene3D:2.10.25.10;PANTHER:PTHR10082;PANTHER:PTHR10082:SF3;SMART:SM00181;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tTTTGTGAGTGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTRAV19\t28664\tBI\tGRCh38\tchr14\t22007900\t22007908\t+\tFrame_Shift_Del\tDEL\tGGTAACTCA\tGGTAACTCA\tATTTC\tnovel\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.69_77delinsATTTC\tp.Val24PhefsTer15\tp.V24Ffs*15\tENST00000390447\t2/2\t25\t6\t19\t22\t\t\tTRAV19,frameshift_variant,p.V24Ffs*15,ENST00000390447,,c.69_77delinsATTTC,HIGH,YES,,,1;TRAV18,downstream_gene_variant,,ENST00000390446,,,MODIFIER,YES,,,1;AC245505.2,upstream_gene_variant,,ENST00000553572,,,MODIFIER,YES,,,1\tATTTC\tENSG00000211799\tENST00000390447\tTranscript\tframeshift_variant\tframeshift_variant\t186-194/467\t69-77/350\t23-26/116\tKVTQ/KFX\taaGGTAACTCAa/aaATTTCa\t\t\t1\tTRAV19\tHGNC\tHGNC:12115\tTR_V_gene\tYES\t\tENSP00000452148\tA0A0A6YYK7.37\t\tUPI0003F47A83\t\t\t\tP1\tcds_end_NF\t\t\t2/2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tHIGH\t1\tindel\t\t\t\t\tCAGAAGGTAACTCAAGCGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse*;pindel\nHAUS4\t54930\tBI\tGRCh38\tchr14\t22946655\t22946655\t+\tMissense_Mutation\tSNP\tC\tC\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.962G>T\tp.Arg321Ile\tp.R321I\tENST00000206474\t10/10\t70\t54\t16\t35\t\t\tHAUS4,missense_variant,p.R321I,ENST00000206474,,c.962G>T,MODERATE,YES,deleterious(0),possibly_damaging(0.549),-1;HAUS4,missense_variant,p.R321I,ENST00000541587,NM_001166269.1&NM_017815.3,c.962G>T,MODERATE,,deleterious(0),possibly_damaging(0.549),-1;HAUS4,missense_variant,p.R276I,ENST00000555986,,c.827G>T,MODERATE,,deleterious(0),possibly_damaging(0.549),-1;HAUS4,missense_variant,p.R276I,ENST00000342454,NM_001166270.2,c.827G>T,MODERATE,,deleterious(0),possibly_damaging(0.549),-1;HAUS4,missense_variant,p.R276I,ENST00000555367,,c.827G>T,MODERATE,,deleterious(0),possibly_damaging(0.549),-1;HAUS4,missense_variant,p.R197I,ENST00000490506,,c.590G>T,MODERATE,,deleterious(0),possibly_damaging(0.549),-1;HAUS4,missense_variant,p.R195I,ENST00000347758,,c.584G>T,MODERATE,,deleterious(0.02),possibly_damaging(0.607),-1;AL132780.3,missense_variant,p.R151I,ENST00000555074,,c.452G>T,MODERATE,YES,deleterious(0),possibly_damaging(0.747),-1;HAUS4,downstream_gene_variant,,ENST00000553420,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000554406,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000554516,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000555040,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000556915,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000557591,,,MODIFIER,,,,-1;HAUS4,non_coding_transcript_exon_variant,,ENST00000554446,,n.703G>T,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000553794,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000554349,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000554373,,,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000554651,,,MODIFIER,,,,-1;HAUS4,3_prime_UTR_variant,,ENST00000553859,,c.*129G>T,MODIFIER,,,,-1;HAUS4,non_coding_transcript_exon_variant,,ENST00000556421,,n.757G>T,MODIFIER,,,,-1;HAUS4,downstream_gene_variant,,ENST00000554063,,,MODIFIER,,,,-1;AL132780.1,intron_variant,,ENST00000548322,,n.159-8475C>A,MODIFIER,,,,1;AL132780.1,intron_variant,,ENST00000548819,,n.195-7676C>A,MODIFIER,,,,1;AL132780.1,intron_variant,,ENST00000668190,,n.147-7676C>A,MODIFIER,YES,,,1\tA\tENSG00000092036\tENST00000206474\tTranscript\tmissense_variant\tmissense_variant\t1215/1642\t962/1092\t321/363\tR/I\taGa/aTa\tCOSV99247140\t\t-1\tHAUS4\tHGNC\tHGNC:20163\tprotein_coding\tYES\tCCDS9580.1\tENSP00000206474\tQ9H6D7.150\t\tUPI000006F422\tQ9H6D7-1\t\t\tP1\t\tdeleterious(0)\tpossibly_damaging(0.549)\t10/10\t\tPANTHER:PTHR16219;Pfam:PF14735\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCCTGTCTTGAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nAJUBA\t84962\tBI\tGRCh38\tchr14\t22981513\t22981514\t+\tFrame_Shift_Ins\tINS\t-\t-\tG\tnovel\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.753dup\tp.Glu253GlyfsTer53\tp.E253Gfs*53\tENST00000262713\t1/8\t23\t4\t18\t14\t\t\tAJUBA,frameshift_variant,p.E253Gfs*53,ENST00000262713,NM_032876.6,c.753dup,HIGH,YES,,,-1;AJUBA,frameshift_variant,p.E253Gfs*53,ENST00000361265,,c.753dup,HIGH,,,,-1;AJUBA,frameshift_variant,p.E27Gfs*53,ENST00000553736,NM_001289097.2,c.73dup,HIGH,,,,-1;AL132780.3,intron_variant,,ENST00000555074,,c.50+695dup,MODIFIER,YES,,,-1;C14orf93,downstream_gene_variant,,ENST00000299088,NM_001130708.3&NM_021944.4,,MODIFIER,YES,,,-1;AJUBA,upstream_gene_variant,,ENST00000397388,NM_198086.3,,MODIFIER,,,,-1;AJUBA,upstream_gene_variant,,ENST00000553592,,,MODIFIER,,,,-1;AJUBA,upstream_gene_variant,,ENST00000553911,,,MODIFIER,,,,-1;AJUBA,upstream_gene_variant,,ENST00000556731,,,MODIFIER,,,,-1;AL132780.2,upstream_gene_variant,,ENST00000555294,,,MODIFIER,,,,1;AL132780.2,upstream_gene_variant,,ENST00000556503,,,MODIFIER,,,,1;AL132780.2,upstream_gene_variant,,ENST00000557615,,,MODIFIER,YES,,,1\tG\tENSG00000129474\tENST00000262713\tTranscript\tframeshift_variant\tframeshift_variant\t1038-1039/4168\t753-754/1617\t251-252/538\t-/X\t-/C\t\t\t-1\tAJUBA\tHGNC\tHGNC:20250\tprotein_coding\tYES\tCCDS9581.1\tENSP00000262713\tQ96IF1.163\t\tUPI0000040AEC\tQ96IF1-1\tNM_032876.6\tNM_032876.6\tP1\t\t\t\t1/8\t\tPANTHER:PTHR24219;PANTHER:PTHR24219:SF7;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tHIGH\t1\tinsertion\t1\t\t\t\tCTCCAAGGGCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmutect2;varscan2\nMYH6\t4624\tBI\tGRCh38\tchr14\t23383284\t23383284\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.5602G>A\tp.Asp1868Asn\tp.D1868N\tENST00000405093\t37/39\t174\t98\t76\t95\t\t\tMYH6,missense_variant,p.D1868N,ENST00000405093,NM_002471.4,c.5602G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.689),-1;CMTM5,downstream_gene_variant,,ENST00000339180,NM_001288746.2,,MODIFIER,YES,,,1;CMTM5,downstream_gene_variant,,ENST00000342473,NM_001288745.2,,MODIFIER,,,,1;CMTM5,downstream_gene_variant,,ENST00000359320,NM_138460.3,,MODIFIER,,,,1;CMTM5,downstream_gene_variant,,ENST00000382809,NM_001037288.2,,MODIFIER,,,,1;CMTM5,downstream_gene_variant,,ENST00000397227,NM_001288744.2,,MODIFIER,,,,1;CMTM5,downstream_gene_variant,,ENST00000555731,,,MODIFIER,,,,1;CMTM5,downstream_gene_variant,,ENST00000649278,,,MODIFIER,,,,1;MYH6,non_coding_transcript_exon_variant,,ENST00000651452,,n.829G>A,MODIFIER,,,,-1;CMTM5,downstream_gene_variant,,ENST00000553750,,,MODIFIER,,,,1;CMTM5,downstream_gene_variant,,ENST00000555487,,,MODIFIER,,,,1\tT\tENSG00000197616\tENST00000405093\tTranscript\tmissense_variant\tmissense_variant\t5669/5940\t5602/5820\t1868/1939\tD/N\tGac/Aac\tCOSV100198199\t\t-1\tMYH6\tHGNC\tHGNC:7576\tprotein_coding\tYES\tCCDS9600.1\tENSP00000386041\tP13533.210\t\tUPI0000160969\t\tNM_002471.4\tNM_002471.4\tP1\t\tdeleterious(0.01)\tpossibly_damaging(0.689)\t37/39\t\tCoiled-coils_(Ncoils):Coil;Pfam:PF01576;PANTHER:PTHR45615;PANTHER:PTHR45615:SF11;Superfamily:SSF57997\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t5\t\t1\t1\tCAGGTCCTGTA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTOGARAM1\t23116\tBI\tGRCh38\tchr14\t44964136\t44964136\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1715G>C\tp.Arg572Thr\tp.R572T\tENST00000361577\t1/19\t176\t155\t21\t94\t\t\tTOGARAM1,missense_variant,p.R572T,ENST00000361462,NM_001308120.2,c.1715G>C,MODERATE,YES,deleterious(0),probably_damaging(0.996),1;TOGARAM1,missense_variant,p.R572T,ENST00000361577,NM_015091.4,c.1715G>C,MODERATE,,deleterious(0),probably_damaging(0.998),1;KLHL28,intron_variant,,ENST00000556239,,c.-1+14062C>G,MODIFIER,,,,-1;KLHL28,upstream_gene_variant,,ENST00000355081,NM_001308112.2,,MODIFIER,YES,,,-1;KLHL28,upstream_gene_variant,,ENST00000396128,NM_017658.5,,MODIFIER,,,,-1;KLHL28,upstream_gene_variant,,ENST00000556500,,,MODIFIER,,,,-1;KLHL28,upstream_gene_variant,,ENST00000557468,,,MODIFIER,,,,-1;KLHL28,upstream_gene_variant,,ENST00000579157,,,MODIFIER,,,,-1;KLHL28,intron_variant,,ENST00000553817,,n.309-44C>G,MODIFIER,,,,-1;TOGARAM1,missense_variant,p.R572T,ENST00000557423,,c.1715G>C,MODERATE,,deleterious(0),probably_damaging(1),1;TOGARAM1,non_coding_transcript_exon_variant,,ENST00000555607,,n.1923G>C,MODIFIER,,,,1;TOGARAM1,non_coding_transcript_exon_variant,,ENST00000555945,,n.1918G>C,MODIFIER,,,,1\tC\tENSG00000198718\tENST00000361577\tTranscript\tmissense_variant\tmissense_variant\t1929/6247\t1715/5163\t572/1720\tR/T\taGa/aCa\tCOSV100753296;COSV61888471\t\t1\tTOGARAM1\tHGNC\tHGNC:19959\tprotein_coding\t\tCCDS9681.1\tENSP00000355045\tQ9Y4F4.145\t\tUPI00001C1F79\tQ9Y4F4-1\tNM_015091.4\t\t\t\tdeleterious(0)\tprobably_damaging(0.998)\t1/19\t\tGene3D:1.25.10.10;PANTHER:PTHR21567;PANTHER:PTHR21567:SF6;SMART:SM01349;Superfamily:SSF48371\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1;1\t\tGGCCAGATTGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nARID4A\t5926\tBI\tGRCh38\tchr14\t58371889\t58371889\t+\tMissense_Mutation\tSNP\tC\tC\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.3674C>A\tp.Ser1225Tyr\tp.S1225Y\tENST00000355431\t24/24\t46\t42\t4\t31\t\t\tARID4A,missense_variant,p.S1225Y,ENST00000355431,NM_002892.4,c.3674C>A,MODERATE,YES,deleterious(0),probably_damaging(0.991),1;ARID4A,missense_variant,p.S1156Y,ENST00000431317,,c.3467C>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;ARID4A,missense_variant,p.S1156Y,ENST00000348476,NM_023001.2,c.3467C>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;ARID4A,missense_variant,p.S1171Y,ENST00000395168,NM_023000.2,c.3512C>A,MODERATE,,deleterious(0),probably_damaging(0.998),1;ARID4A,non_coding_transcript_exon_variant,,ENST00000466065,,n.299C>A,MODIFIER,,,,1;AL139021.2,intron_variant,,ENST00000556390,,n.342-1809G>T,MODIFIER,YES,,,-1\tA\tENSG00000032219\tENST00000355431\tTranscript\tmissense_variant\tmissense_variant\t3877/5864\t3674/3774\t1225/1257\tS/Y\ttCt/tAt\tCOSV100794625\t\t1\tARID4A\tHGNC\tHGNC:9885\tprotein_coding\tYES\tCCDS9732.1\tENSP00000347602\tP29374.184\tA0A024R657.53\tUPI000013FD01\tP29374-1\tNM_002892.4\tNM_002892.4\tP2\t\tdeleterious(0)\tprobably_damaging(0.991)\t24/24\t\tPANTHER:PTHR13964;PANTHER:PTHR13964:SF26;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tAGTGTCTCATG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nKCNH5\t27133\tBI\tGRCh38\tchr14\t62802558\t62802558\t+\tMissense_Mutation\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1593C>A\tp.Asp531Glu\tp.D531E\tENST00000322893\t9/11\t78\t36\t41\t57\t\t\tKCNH5,missense_variant,p.D531E,ENST00000322893,NM_139318.5,c.1593C>A,MODERATE,YES,deleterious(0.01),probably_damaging(0.96),-1;KCNH5,missense_variant,p.D531E,ENST00000420622,NM_172375.3,c.1593C>A,MODERATE,,tolerated(0.27),benign(0.266),-1;KCNH5,missense_variant,p.D473E,ENST00000394968,,c.1419C>A,MODERATE,,tolerated(0.1),benign(0.187),-1\tT\tENSG00000140015\tENST00000322893\tTranscript\tmissense_variant\tmissense_variant\t1865/11283\t1593/2967\t531/988\tD/E\tgaC/gaA\tCOSV100528116\t\t-1\tKCNH5\tHGNC\tHGNC:6254\tprotein_coding\tYES\tCCDS9756.1\tENSP00000321427\tQ8NCM2.170\t\tUPI0000039E2D\tQ8NCM2-1\tNM_139318.5\tNM_139318.5\tP1\t\tdeleterious(0.01)\tprobably_damaging(0.96)\t9/11\t\tGene3D:2.60.120.10;Prints:PR01464;PANTHER:PTHR10217;PANTHER:PTHR10217:SF533;Superfamily:SSF51206\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t1\tCTCATGTCCTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPCNX1\t22990\tBI\tGRCh38\tchr14\t70988690\t70988690\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2435C>T\tp.Ser812Leu\tp.S812L\tENST00000304743\t7/36\t298\t270\t28\t166\t\t\tPCNX1,missense_variant,p.S812L,ENST00000304743,NM_014982.3,c.2435C>T,MODERATE,YES,deleterious(0),benign(0.086),1;PCNX1,intron_variant,,ENST00000439984,NM_001308160.2,c.2311+10042C>T,MODIFIER,,,,1;PCNX1,non_coding_transcript_exon_variant,,ENST00000554879,,n.2881C>T,MODIFIER,,,,1;PCNX1,intron_variant,,ENST00000556846,,n.271+10042C>T,MODIFIER,,,,1\tT\tENSG00000100731\tENST00000304743\tTranscript\tmissense_variant\tmissense_variant\t2827/12865\t2435/7026\t812/2341\tS/L\ttCa/tTa\tCOSV99457178\t\t1\tPCNX1\tHGNC\tHGNC:19740\tprotein_coding\tYES\tCCDS9806.1\tENSP00000304192\tQ96RV3.134\t\tUPI000013E9BB\tQ96RV3-1\tNM_014982.3\tNM_014982.3\tP4\t\tdeleterious(0)\tbenign(0.086)\t7/36\t\tPANTHER:PTHR12372;PANTHER:PTHR12372:SF2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCGGATCACCCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nDCAF4\t26094\tBI\tGRCh38\tchr14\t72945970\t72945970\t+\tSilent\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.621G>T\tp.Leu207=\tp.L207=\tENST00000358377\t7/14\t439\t255\t184\t240\t\t\tDCAF4,synonymous_variant,p.L107=,ENST00000553457,,c.321G>T,LOW,,,,1;DCAF4,synonymous_variant,p.L207=,ENST00000358377,NM_001352448.2&NM_001352449.2&NM_015604.4&NM_001163509.2,c.621G>T,LOW,YES,,,1;DCAF4,synonymous_variant,p.L207=,ENST00000555042,NM_001163508.2,c.621G>T,LOW,,,,1;DCAF4,synonymous_variant,p.L107=,ENST00000394234,NM_181340.3,c.321G>T,LOW,,,,1;DCAF4,synonymous_variant,p.L146=,ENST00000353777,,c.438G>T,LOW,,,,1;DCAF4,synonymous_variant,p.L146=,ENST00000509153,NM_001352447.2&NM_181341.3,c.438G>T,LOW,,,,1;DCAF4,downstream_gene_variant,,ENST00000508412,,,MODIFIER,,,,1;DCAF4,downstream_gene_variant,,ENST00000513337,,,MODIFIER,,,,1;DCAF4,downstream_gene_variant,,ENST00000514486,,,MODIFIER,,,,1;DCAF4,3_prime_UTR_variant,,ENST00000509320,,c.*360G>T,MODIFIER,,,,1;DCAF4,non_coding_transcript_exon_variant,,ENST00000557203,,n.465G>T,MODIFIER,,,,1;DCAF4,downstream_gene_variant,,ENST00000505361,,,MODIFIER,,,,1\tT\tENSG00000119599\tENST00000358377\tTranscript\tsynonymous_variant\tsynonymous_variant\t709/2474\t621/1488\t207/495\tL\tctG/ctT\tCOSV100611170\t\t1\tDCAF4\tHGNC\tHGNC:20229\tprotein_coding\tYES\tCCDS9809.1\tENSP00000351147\tQ8WV16.152\t\tUPI000000CBDC\tQ8WV16-1\tNM_001352448.2;NM_001352449.2;NM_015604.4;NM_001163509.2\tNM_015604.4\tP4\t\t\t\t7/14\t\tGene3D:2.130.10.10;PANTHER:PTHR44472\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tAGTCTGAAGAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPAPOLA\t10914\tBI\tGRCh38\tchr14\t96532383\t96532383\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.660C>T\tp.Phe220=\tp.F220=\tENST00000216277\t8/22\t92\t78\t14\t54\t\t\tPAPOLA,synonymous_variant,p.F220=,ENST00000216277,NM_032632.4&NM_001293627.1&NM_001293632.2&NM_001293628.1,c.660C>T,LOW,YES,,,1;PAPOLA,synonymous_variant,p.F220=,ENST00000557320,NM_001252006.1,c.660C>T,LOW,,,,1;PAPOLA,synonymous_variant,p.F220=,ENST00000392990,NM_001363662.2&NM_001363665.2&NM_001363664.2&NM_001363666.2,c.660C>T,LOW,,,,1;PAPOLA,synonymous_variant,p.F106=,ENST00000553461,,c.318C>T,LOW,,,,1;PAPOLA,downstream_gene_variant,,ENST00000556619,,,MODIFIER,,,,1;PAPOLA,downstream_gene_variant,,ENST00000557471,NM_001252007.1,,MODIFIER,,,,1;PAPOLA,non_coding_transcript_exon_variant,,ENST00000555626,,n.756C>T,MODIFIER,,,,1;PAPOLA,non_coding_transcript_exon_variant,,ENST00000618976,,n.877C>T,MODIFIER,,,,1;PAPOLA,downstream_gene_variant,,ENST00000553357,,,MODIFIER,,,,1;PAPOLA,downstream_gene_variant,,ENST00000554130,,,MODIFIER,,,,1;PAPOLA,downstream_gene_variant,,ENST00000554887,,,MODIFIER,,,,1;PAPOLA,3_prime_UTR_variant,,ENST00000553689,,c.*160C>T,MODIFIER,,,,1;PAPOLA,non_coding_transcript_exon_variant,,ENST00000555224,,n.311C>T,MODIFIER,,,,1;PAPOLA,upstream_gene_variant,,ENST00000554666,,,MODIFIER,,,,1;PAPOLA,upstream_gene_variant,,ENST00000555021,,,MODIFIER,,,,1;PAPOLA,upstream_gene_variant,,ENST00000555131,,,MODIFIER,,,,1;PAPOLA,downstream_gene_variant,,ENST00000555912,,,MODIFIER,,,,1;PAPOLA,downstream_gene_variant,,ENST00000557406,,,MODIFIER,,,,1\tT\tENSG00000090060\tENST00000216277\tTranscript\tsynonymous_variant\tsynonymous_variant\t880/4519\t660/2238\t220/745\tF\tttC/ttT\tCOSV99354639\t\t1\tPAPOLA\tHGNC\tHGNC:14981\tprotein_coding\tYES\tCCDS9946.1\tENSP00000216277\tP51003.192\tA0A024R6M3.51\tUPI0000074269\tP51003-1\tNM_032632.4;NM_001293627.1;NM_001293632.2;NM_001293628.1\t\tP3\t\t\t\t8/22\t\tGene3D:1.10.1410.10;Pfam:PF04928;PIRSF:PIRSF018425;PANTHER:PTHR10682;PANTHER:PTHR10682:SF9;Superfamily:SSF81631\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tAACTTCAGGTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSNORD114-5\t767581\tBI\tGRCh38\tchr14\t100955385\t100955385\t+\tRNA\tSNP\tC\tC\tT\tnovel\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tn.16C>T\t\t\tENST00000362928\t1/1\t95\t73\t22\t63\t\t\tSNORD114-5,non_coding_transcript_exon_variant,,ENST00000362928,,n.16C>T,MODIFIER,YES,,,1;AL132709.1,upstream_gene_variant,,ENST00000363280,,,MODIFIER,YES,,,1;SNORD114-2,downstream_gene_variant,,ENST00000363953,,,MODIFIER,YES,,,1;SNORD114-4,downstream_gene_variant,,ENST00000363962,,,MODIFIER,YES,,,1;SNORD114-6,upstream_gene_variant,,ENST00000364393,,,MODIFIER,YES,,,1;SNORD114-3,downstream_gene_variant,,ENST00000364969,,,MODIFIER,YES,,,1;MEG8,intron_variant,,ENST00000414488,,n.446+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000434716,,n.399+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000554369,,n.219+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000556637,,n.399+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000638012,,n.3236+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000655773,,n.601+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000656987,,n.882+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000663218,,n.1576+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000666001,,n.353+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000667814,,n.786+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000668102,,n.1852+379C>T,MODIFIER,,,,1;MEG8,intron_variant,,ENST00000668725,,n.3289+379C>T,MODIFIER,,,,1;MEG8,downstream_gene_variant,,ENST00000427085,,,MODIFIER,,,,1;MEG8,upstream_gene_variant,,ENST00000443252,,,MODIFIER,,,,1;MEG8,upstream_gene_variant,,ENST00000649300,,,MODIFIER,,,,1;MEG8,downstream_gene_variant,,ENST00000653102,,,MODIFIER,,,,1;MEG8,upstream_gene_variant,,ENST00000660698,,,MODIFIER,,,,1;MEG8,downstream_gene_variant,,ENST00000661496,,,MODIFIER,,,,1;MEG8,upstream_gene_variant,,ENST00000666972,,,MODIFIER,YES,,,1\tT\tENSG00000199798\tENST00000362928\tTranscript\tnon_coding_transcript_exon_variant\tnon_coding_transcript_exon_variant\t16/70\t\t\t\t\t\t\t1\tSNORD114-5\tHGNC\tHGNC:32993\tsnoRNA\tYES\t\t\t\t\t\t\t\t\t\t\t\t\t1/1\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tmiRNA_stem\tMODIFIER\t1\tSNV\t\t\t\t\tATGACCACTGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nAHNAK2\t113146\tBI\tGRCh38\tchr14\t104954518\t104954518\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.933G>A\tp.Gln311=\tp.Q311=\tENST00000333244\t7/7\t54\t47\t6\t25\t\t\tAHNAK2,synonymous_variant,p.Q311=,ENST00000333244,NM_138420.4&NM_001350929.2,c.933G>A,LOW,YES,,,-1;AHNAK2,upstream_gene_variant,,ENST00000557457,,,MODIFIER,,,,-1;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555122,,n.1061G>A,MODIFIER,,,,-1;AHNAK2,non_coding_transcript_exon_variant,,ENST00000555544,,n.728G>A,MODIFIER,,,,-1\tT\tENSG00000185567\tENST00000333244\tTranscript\tsynonymous_variant\tsynonymous_variant\t1070/18335\t933/17388\t311/5795\tQ\tcaG/caA\tCOSV100318919\t\t-1\tAHNAK2\tHGNC\tHGNC:20125\tprotein_coding\tYES\tCCDS45177.1\tENSP00000353114\tQ8IVF2.128\t\tUPI00015BB2CA\tQ8IVF2-1\tNM_138420.4;NM_001350929.2\tNM_138420.4\tP1\t\t\t\t7/7\t\tPANTHER:PTHR23348;PANTHER:PTHR23348:SF37;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t5\t\t1\t\tGCCTTCTGCTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nGOLGA6L22\t440243\tBI\tGRCh38\tchr15\t22460889\t22460889\t+\tMissense_Mutation\tSNP\tA\tA\tG\tnovel\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.121A>G\tp.Ile41Val\tp.I41V\tENST00000622895\t2/9\t203\t188\t15\t160\t\t\tGOLGA6L22,missense_variant,p.I41V,ENST00000622895,,c.121A>G,MODERATE,YES,deleterious(0.01),probably_damaging(0.953),1;GOLGA6L22,missense_variant,p.I84V,ENST00000620691,,c.250A>G,MODERATE,,deleterious(0.04),possibly_damaging(0.625),1\tG\tENSG00000277865\tENST00000622895\tTranscript\tmissense_variant\tmissense_variant\t121/4178\t121/2433\t41/810\tI/V\tAta/Gta\t\t\t1\tGOLGA6L22\tHGNC\tHGNC:50289\tprotein_coding\tYES\t\tENSP00000483673\tH0YM25.52\t\tUPI0004620C46\t\t\t\tP4\t\tdeleterious(0.01)\tprobably_damaging(0.953)\t2/9\t\tPANTHER:PTHR23143;PANTHER:PTHR23143:SF20;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t5\t\t\t\tAGAAAATAAAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nMKRN3\t7681\tBI\tGRCh38\tchr15\t23567291\t23567291\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1509C>T\tp.Phe503=\tp.F503=\tENST00000314520\t1/1\t143\t122\t20\t78\t\t\tMKRN3,synonymous_variant,p.F503=,ENST00000314520,NM_005664.4,c.1509C>T,LOW,YES,,,1;MKRN3,3_prime_UTR_variant,,ENST00000678440,,c.*448C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000564592,,c.482+307C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000568252,,c.305+1204C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000647595,,c.51+1458C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000649065,,c.482+307C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000676568,,c.927+582C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000677119,,c.305+1204C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000679144,,c.305+1204C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000570112,,n.333+307C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000568945,,c.*141+307C>T,MODIFIER,,,,1;MKRN3,intron_variant,,ENST00000677372,,c.*141+307C>T,MODIFIER,,,,1;AC126407.1,non_coding_transcript_exon_variant,,ENST00000563044,,n.539G>A,MODIFIER,YES,,,-1\tT\tENSG00000179455\tENST00000314520\tTranscript\tsynonymous_variant\tsynonymous_variant\t1618/2371\t1509/1524\t503/507\tF\tttC/ttT\tCOSV58811959\t\t1\tMKRN3\tHGNC\tHGNC:7114\tprotein_coding\tYES\tCCDS10013.1\tENSP00000313881\tQ13064.172\t\tUPI000000DAA1\t\tNM_005664.4\tNM_005664.4\tP1\t\t\t\t1/1\t\tPfam:PF15815\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t\t\t1\t1\tTATTTCAATTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM3500012\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nATP10A\t57194\tBI\tGRCh38\tchr15\t25679815\t25679815\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.4026G>A\tp.Arg1342=\tp.R1342=\tENST00000356865\t22/22\t108\t75\t33\t130\t\t\tATP10A,synonymous_variant,p.R1342=,ENST00000555815,NM_024490.3,c.4026G>A,LOW,YES,,,-1;ATP10A,synonymous_variant,p.R1342=,ENST00000356865,,c.4026G>A,LOW,,,,-1;ATP10A,downstream_gene_variant,,ENST00000555756,,,MODIFIER,,,,-1;ATP10A,non_coding_transcript_exon_variant,,ENST00000673680,,n.4688G>A,MODIFIER,,,,-1;ATP10A,downstream_gene_variant,,ENST00000674138,,,MODIFIER,,,,-1;ATP10A,non_coding_transcript_exon_variant,,ENST00000673805,,n.3371G>A,MODIFIER,,,,-1;ATP10A,non_coding_transcript_exon_variant,,ENST00000674021,,n.2353G>A,MODIFIER,,,,-1;ATP10A,non_coding_transcript_exon_variant,,ENST00000555450,,n.1818G>A,MODIFIER,,,,-1\tT\tENSG00000206190\tENST00000356865\tTranscript\tsynonymous_variant\tsynonymous_variant\t4225/6767\t4026/4500\t1342/1499\tR\tagG/agA\tCOSV100791532\t\t-1\tATP10A\tHGNC\tHGNC:13542\tprotein_coding\t\tCCDS32178.1\tENSP00000349325\tO60312.194\t\tUPI0000124FAB\tO60312-1\t\t\tP1\t\t\t\t22/22\t\tMobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t1\t1\tACTGTCCTCCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nIVD\t3712\tBI\tGRCh38\tchr15\t40410643\t40410643\t+\tMissense_Mutation\tSNP\tC\tC\tG\tnovel\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.311C>G\tp.Ser104Cys\tp.S104C\tENST00000651168\t4/12\t110\t64\t45\t149\t\t\tIVD,missense_variant,p.S104C,ENST00000651168,,c.311C>G,MODERATE,YES,deleterious(0.05),possibly_damaging(0.552),1;IVD,missense_variant,p.S74C,ENST00000650656,,c.221C>G,MODERATE,,deleterious(0.03),possibly_damaging(0.874),1;IVD,missense_variant,p.S101C,ENST00000487418,NM_001354600.3&NM_001354598.3&NM_001354601.3&NM_001354597.3&NM_001354599.3&NM_002225.5,c.302C>G,MODERATE,,deleterious(0.05),possibly_damaging(0.585),1;IVD,missense_variant,p.S71C,ENST00000479013,NM_001159508.3,c.212C>G,MODERATE,,deleterious(0.03),possibly_damaging(0.874),1;IVD,missense_variant,p.S21C,ENST00000473112,,c.62C>G,MODERATE,,deleterious_low_confidence(0),possibly_damaging(0.816),1;IVD,missense_variant,p.S85C,ENST00000558610,,c.254C>G,MODERATE,,deleterious(0.01),possibly_damaging(0.75),1;IVD,missense_variant,p.S130C,ENST00000610693,,c.389C>G,MODERATE,,deleterious(0.03),possibly_damaging(0.887),1;IVD,upstream_gene_variant,,ENST00000491554,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000497252,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000481262,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000484250,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000497816,,,MODIFIER,,,,1;IVD,upstream_gene_variant,,ENST00000560660,,,MODIFIER,,,,1\tG\tENSG00000128928\tENST00000651168\tTranscript\tmissense_variant\tmissense_variant\t645/4665\t311/1281\t104/426\tS/C\ttCc/tGc\t\t\t1\tIVD\tHGNC\tHGNC:6186\tprotein_coding\tYES\tCCDS10057.2\tENSP00000499074\tP26440.204\t\tUPI0000D4AF3D\tP26440-1\t\t\tA1\t\tdeleterious(0.05)\tpossibly_damaging(0.552)\t4/12\t\tCDD:cd01156;PANTHER:PTHR43884;PANTHER:PTHR43884:SF10;Gene3D:1.10.540.10;Pfam:PF02771;Superfamily:SSF56645\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t\t\t\t1\tCGGCTCCGGCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nLRRC49\t54839\tBI\tGRCh38\tchr15\t71049448\t71049448\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1897G>A\tp.Glu633Lys\tp.E633K\tENST00000260382\t16/16\t57\t33\t24\t81\t\t\tLRRC49,missense_variant,p.E623K,ENST00000544974,NM_001284357.1,c.1867G>A,MODERATE,,tolerated(0.56),benign(0.013),1;LRRC49,missense_variant,p.E633K,ENST00000260382,NM_017691.5,c.1897G>A,MODERATE,,tolerated(0.47),benign(0),1;LRRC49,missense_variant,p.E589K,ENST00000443425,NM_001199018.2,c.1765G>A,MODERATE,,tolerated(0.58),benign(0.003),1;LRRC49,missense_variant,p.E638K,ENST00000560369,NM_001199017.2,c.1912G>A,MODERATE,YES,tolerated(0.47),benign(0.003),1;LRRC49,missense_variant,p.E339K,ENST00000560691,NM_001363732.1,c.1015G>A,MODERATE,,tolerated(0.56),benign(0),1;LRRC49,missense_variant,p.E321K,ENST00000560158,,c.961G>A,MODERATE,,tolerated(0.61),benign(0),1;LRRC49,non_coding_transcript_exon_variant,,ENST00000436542,,n.2113G>A,MODIFIER,,,,1;LRRC49,non_coding_transcript_exon_variant,,ENST00000561131,,n.111G>A,MODIFIER,,,,1;LRRC49,3_prime_UTR_variant,,ENST00000561081,,c.*1761G>A,MODIFIER,,,,1;LRRC49,3_prime_UTR_variant,,ENST00000560107,,c.*1590G>A,MODIFIER,,,,1\tA\tENSG00000137821\tENST00000260382\tTranscript\tmissense_variant\tmissense_variant\t1966/6176\t1897/2061\t633/686\tE/K\tGaa/Aaa\tCOSV53015401\t\t1\tLRRC49\tHGNC\tHGNC:25965\tprotein_coding\t\tCCDS32282.1\tENSP00000260382\tQ8IUZ0.145\t\tUPI000013F990\tQ8IUZ0-1\tNM_017691.5\tNM_017691.5\tP1\t\ttolerated(0.47)\tbenign(0)\t16/16\t\tCoiled-coils_(Ncoils):Coil;PANTHER:PTHR15454;PANTHER:PTHR15454:SF23\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tATATAGAAGAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM3988096\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCELF6\t60677\tBI\tGRCh38\tchr15\t72287378\t72287378\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1333G>A\tp.Asp445Asn\tp.D445N\tENST00000287202\t12/13\t80\t57\t23\t110\t\t\tCELF6,missense_variant,p.D445N,ENST00000287202,NM_052840.5,c.1333G>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;CELF6,missense_variant,p.D332N,ENST00000395258,,c.994G>A,MODERATE,,deleterious(0),benign(0.203),-1;CELF6,missense_variant,p.D308N,ENST00000543764,NM_001172685.1,c.922G>A,MODERATE,,deleterious(0),probably_damaging(0.99),-1;CELF6,missense_variant,p.D418N,ENST00000567083,NM_001172684.1,c.1252G>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;AC009690.3,missense_variant,p.D445N,ENST00000569547,,c.1333G>A,MODERATE,YES,deleterious(0),probably_damaging(0.998),-1;AC009690.1,3_prime_UTR_variant,,ENST00000379915,,c.*1924G>A,MODIFIER,YES,,,-1;CELF6,3_prime_UTR_variant,,ENST00000437872,,c.*795G>A,MODIFIER,,,,-1;AC009690.2,intron_variant,,ENST00000570175,,n.165+8347C>T,MODIFIER,YES,,,1\tT\tENSG00000140488\tENST00000287202\tTranscript\tmissense_variant\tmissense_variant\t1616/3373\t1333/1446\t445/481\tD/N\tGac/Aac\tCOSV99764168\t\t-1\tCELF6\tHGNC\tHGNC:14059\tprotein_coding\tYES\tCCDS10242.1\tENSP00000287202\tQ96J87.152\t\tUPI000006F0AA\tQ96J87-1\tNM_052840.5\tNM_052840.5\tP1\t\tdeleterious(0)\tprobably_damaging(0.998)\t12/13\t\tGene3D:3.30.70.330;Pfam:PF00076;PROSITE_profiles:PS50102;PANTHER:PTHR24012;PANTHER:PTHR24012:SF716;SMART:SM00360;Superfamily:SSF54928;CDD:cd12639\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tATTGTCAAAAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF774\t342132\tBI\tGRCh38\tchr15\t90360987\t90360987\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs530118133\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1156G>A\tp.Asp386Asn\tp.D386N\tENST00000354377\t4/4\t93\t70\t23\t74\t\t\tZNF774,missense_variant,p.D386N,ENST00000354377,NM_001004309.3,c.1156G>A,MODERATE,YES,tolerated(0.36),benign(0.109),1;ZNF774,intron_variant,,ENST00000379090,,c.212-1558G>A,MODIFIER,,,,1;ZNF774,downstream_gene_variant,,ENST00000558586,,,MODIFIER,,,,1;ZNF774,downstream_gene_variant,,ENST00000558115,,,MODIFIER,,,,1;ZNF774,downstream_gene_variant,,ENST00000560038,,,MODIFIER,,,,1\tA\tENSG00000196391\tENST00000354377\tTranscript\tmissense_variant\tmissense_variant\t1303/3163\t1156/1452\t386/483\tD/N\tGac/Aac\trs530118133;COSV100586467\t\t1\tZNF774\tHGNC\tHGNC:33108\tprotein_coding\tYES\tCCDS32330.1\tENSP00000346348\tQ6NX45.143\t\tUPI00001A73D8\t\tNM_001004309.3\tNM_001004309.3\tP1\t\ttolerated(0.36)\tbenign(0.109)\t4/4\t\tGene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24377;PANTHER:PTHR24377:SF742;SMART:SM00355;Superfamily:SSF57667\t0.0002\t0.0008\t0.0\t0.0\t0.0\t0.0\t\t\t3.979e-06\t6.152e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0008\tAFR\t2.7057400075136684e-05\t7.301760342670605e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.5433499356731772e-05\t0.0\t0.0\t7.301760342670605e-05\tafr\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t0;1\t\tTCGCCGACAGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSV2B\t9899\tBI\tGRCh38\tchr15\t91292429\t91292429\t+\tSilent\tSNP\tC\tC\tT\trs761502738\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1929C>T\tp.Thr643=\tp.T643=\tENST00000330276\t12/12\t145\t121\t24\t83\t\t\tSV2B,synonymous_variant,p.T643=,ENST00000394232,NM_014848.7&NM_001323032.3&NM_001323034.3&NM_001323033.3,c.1929C>T,LOW,YES,,,1;SV2B,synonymous_variant,p.T643=,ENST00000330276,NM_001323031.2&NM_001323037.3&NM_001323038.3&NM_001323039.3,c.1929C>T,LOW,,,,1;SV2B,synonymous_variant,p.T492=,ENST00000545111,NM_001167580.3&NM_001323036.3&NM_001323040.3,c.1476C>T,LOW,,,,1;SV2B,synonymous_variant,p.T643=,ENST00000557410,,c.1929C>T,LOW,,,,1\tT\tENSG00000185518\tENST00000330276\tTranscript\tsynonymous_variant\tsynonymous_variant\t2323/11202\t1929/2052\t643/683\tT\tacC/acT\trs761502738;COSV100370726;COSV100371025\t\t1\tSV2B\tHGNC\tHGNC:16874\tprotein_coding\t\tCCDS10370.1\tENSP00000332818\tQ7L1I2.145\t\tUPI000006FCF1\tQ7L1I2-1\tNM_001323031.2;NM_001323037.3;NM_001323038.3;NM_001323039.3\t\tP1\t\t\t\t12/12\t\tGene3D:1.20.1250.20;Pfam:PF07690;PROSITE_profiles:PS50850;PANTHER:PTHR23511;PANTHER:PTHR23511:SF2;Superfamily:SSF103473;TIGRFAM:TIGR01299;Transmembrane_helices:TMhelix;CDD:cd17438\t\t\t\t\t\t\t\t\t3.977e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.792e-06\t0.0\t0.0\t8.792e-06\tgnomAD_NFE\t6.761139957234263e-06\t2.4326200218638405e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\t\t\t0;1;1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t0;1;1\t\tAACACCATCTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSYNM\t23336\tBI\tGRCh38\tchr15\t99113592\t99113592\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.812G>C\tp.Arg271Thr\tp.R271T\tENST00000336292\t2/4\t47\t25\t22\t23\t\t\tSYNM,missense_variant,p.R271T,ENST00000336292,NM_145728.3,c.812G>C,MODERATE,YES,deleterious(0),probably_damaging(0.948),1;SYNM,missense_variant,p.R271T,ENST00000594047,NM_015286.6,c.812G>C,MODERATE,,deleterious(0),possibly_damaging(0.905),1;SYNM,missense_variant,p.R271T,ENST00000328642,,c.812G>C,MODERATE,,tolerated(0.22),possibly_damaging(0.462),1;SYNM,splice_region_variant,,ENST00000560674,,c.-47G>C,LOW,,,,1\tC\tENSG00000182253\tENST00000336292\tTranscript\tmissense_variant\tmissense_variant;splice_region_variant\t932/7353\t812/4698\t271/1565\tR/T\taGa/aCa\tCOSV100153040\t\t1\tSYNM\tHGNC\tHGNC:24466\tprotein_coding\tYES\tCCDS73787.1\tENSP00000336775\tO15061.160\t\tUPI0000DC3AA9\t\tNM_145728.3\tNM_145728.3\tP3\t\tdeleterious(0)\tprobably_damaging(0.948)\t2/4\t\tGene3D:1.20.5.170;Pfam:PF00038;PROSITE_profiles:PS51842;PANTHER:PTHR47136;SMART:SM01391;Superfamily:SSF64593\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tTTAGAGAGTGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCERS3\t204219\tBI\tGRCh38\tchr15\t100402740\t100402740\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1125C>T\tp.Leu375=\tp.L375=\tENST00000284382\t13/13\t66\t59\t7\t35\t\t\tCERS3,synonymous_variant,p.L375=,ENST00000284382,NM_178842.5&NM_001290343.2&NM_001378789.1,c.1125C>T,LOW,YES,,,-1;CERS3,synonymous_variant,p.L375=,ENST00000394113,NM_001290341.2,c.1125C>T,LOW,,,,-1;CERS3,synonymous_variant,p.L375=,ENST00000538112,NM_001290342.2,c.1125C>T,LOW,,,,-1;CERS3,non_coding_transcript_exon_variant,,ENST00000560944,,n.219C>T,MODIFIER,,,,-1;CERS3-AS1,intron_variant,,ENST00000560643,,n.51+2815G>A,MODIFIER,,,,1;CERS3-AS1,intron_variant,,ENST00000560718,,n.211+2815G>A,MODIFIER,,,,1\tA\tENSG00000154227\tENST00000284382\tTranscript\tsynonymous_variant\tsynonymous_variant\t1549/3894\t1125/1152\t375/383\tL\tctC/ctT\tCOSV99432824\t\t-1\tCERS3\tHGNC\tHGNC:23752\tprotein_coding\tYES\tCCDS10384.1\tENSP00000284382\tQ8IU89.151\t\tUPI00001975AB\t\tNM_178842.5;NM_001290343.2;NM_001378789.1\t\tP1\t\t\t\t13/13\t\tPANTHER:PTHR12560;PANTHER:PTHR12560:SF18\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t1\tGGAATGAGGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nWDR90\t197335\tBI\tGRCh38\tchr16\t666533\t666533\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs371191203\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.4819G>A\tp.Asp1607Asn\tp.D1607N\tENST00000293879\t38/41\t75\t59\t16\t63\t\t\tWDR90,missense_variant,p.D1609N,ENST00000549091,,c.4825G>A,MODERATE,YES,tolerated(0.15),benign(0.029),1;WDR90,missense_variant,p.D1607N,ENST00000293879,NM_145294.5,c.4819G>A,MODERATE,,tolerated(0.15),benign(0.045),1;WDR90,missense_variant,p.D206N,ENST00000547944,,c.616G>A,MODERATE,,tolerated(0.1),benign(0.042),1;WDR90,missense_variant,p.D14N,ENST00000551100,,c.40G>A,MODERATE,,tolerated(0.12),benign(0.029),1;WDR90,intron_variant,,ENST00000315764,,c.538-140G>A,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000315082,NM_001352287.1&NM_001352275.2&NM_001352290.2&NM_138769.3&NM_001352289.2&NM_001352294.2&NM_001352278.2&NM_001352280.2&NM_001352292.2&NM_001352281.2&NM_001352284.2&NM_001352285.2&NM_001352276.2&NM_001352277.2&NM_001352279.2&NM_001352291.2&NM_001352282.2&NM_001352293.2&NM_001352283.2&NM_001352288.2&NM_001352286.2,,MODIFIER,YES,,,1;WDR90,upstream_gene_variant,,ENST00000546896,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000561929,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000563134,,,MODIFIER,,,,1;WDR90,non_coding_transcript_exon_variant,,ENST00000547543,,n.922G>A,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000548603,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000569943,,,MODIFIER,,,,1;WDR90,3_prime_UTR_variant,,ENST00000552728,,c.*1036G>A,MODIFIER,,,,1;WDR90,non_coding_transcript_exon_variant,,ENST00000547407,,n.3179G>A,MODIFIER,,,,1;WDR90,non_coding_transcript_exon_variant,,ENST00000549024,,n.1589G>A,MODIFIER,,,,1;WDR90,non_coding_transcript_exon_variant,,ENST00000553080,,n.1199G>A,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000546516,,,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000546923,,,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000548448,,,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000550902,,,MODIFIER,,,,1;WDR90,downstream_gene_variant,,ENST00000552683,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000561983,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000562333,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000562598,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000562708,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000563637,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000563776,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000565004,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000566214,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000566965,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000567017,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000567589,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000568636,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000568950,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000569358,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000569675,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000569706,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000570092,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000570280,,,MODIFIER,,,,1;RHOT2,upstream_gene_variant,,ENST00000602564,,,MODIFIER,,,,1\tA\tENSG00000161996\tENST00000293879\tTranscript\tmissense_variant\tmissense_variant\t4871/5540\t4819/5247\t1607/1748\tD/N\tGac/Aac\trs371191203;COSV99554149\t\t1\tWDR90\tHGNC\tHGNC:26960\tprotein_coding\t\tCCDS42092.1\tENSP00000293879\tQ96KV7.151\t\tUPI0000D67C48\tQ96KV7-1\tNM_145294.5\tNM_145294.5\tP4\t\ttolerated(0.15)\tbenign(0.045)\t38/41\t\tGene3D:2.130.10.10;PANTHER:PTHR13720;PANTHER:PTHR13720:SF24;Superfamily:SSF50998\t\t\t\t\t\t\t\t\t7.268e-05\t0.0\t0.000116\t0.0\t0.0\t0.0\t0.0\t0.0001664\t0.0004249\t0.0004249\tgnomAD_SAS\t2.0279599993955344e-05\t0.0\t0.0\t6.62339007249102e-05\t0.0\t0.0\t0.0\t0.0032894699834287167\t0.0\t0.0\t0.0002084199950331822\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t5\t\t0;1\t\tCCTCCGACTGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTSC2\t7249\tBI\tGRCh38\tchr16\t2077658\t2077658\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2898C>T\tp.Phe966=\tp.F966=\tENST00000219476\t26/42\t214\t159\t55\t151\t\t\tTSC2,synonymous_variant,p.F966=,ENST00000219476,NM_000548.5,c.2898C>T,LOW,YES,,,1;TSC2,synonymous_variant,p.F966=,ENST00000643946,,c.2898C>T,LOW,,,,1;TSC2,synonymous_variant,p.F966=,ENST00000646388,,c.2898C>T,LOW,,,,1;TSC2,synonymous_variant,p.F966=,ENST00000350773,NM_001114382.2,c.2898C>T,LOW,,,,1;TSC2,synonymous_va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83-4156G>C,MODIFIER,,,,1;ELOB,downstream_gene_variant,,ENST00000262306,NM_207013.3,,MODIFIER,YES,,,-1;ELOB,downstream_gene_variant,,ENST00000409477,,,MODIFIER,,,,-1;ELOB,downstream_gene_variant,,ENST00000409906,NM_007108.4,,MODIFIER,,,,-1;ELOB,downstream_gene_variant,,ENST00000494946,,,MODIFIER,,,,-1;SRRM2,upstream_gene_variant,,ENST00000570539,,,MODIFIER,,,,1;SRRM2,downstream_gene_variant,,ENST00000571378,,,MODIFIER,,,,1;ELOB,downstream_gene_variant,,ENST00000572954,,,MODIFIER,,,,-1;SRRM2,downstream_gene_variant,,ENST00000576924,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000572721,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000573583,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000574593,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000574866,,,MODIFIER,,,,1;SRRM2,downstream_gene_variant,,ENST00000576674,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000570705,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000571041,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000572883,,,MODIFIER,,,,1;SRRM2,downstream_gene_variant,,ENST00000572952,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000573311,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000573692,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000574331,,,MODIFIER,,,,1;SRRM2,upstream_gene_variant,,ENST00000576878,,,MODIFIER,,,,1\tC\tENSG00000167978\tENST00000301740\tTranscript\tmissense_variant\tmissense_variant\t6860/9044\t6620/8259\t2207/2752\tR/T\taGa/aCa\tCOSV99241728\t\t1\tSRRM2\tHGNC\tHGNC:16639\tprotein_coding\tYES\tCCDS32373.1\tENSP00000301740\tQ9UQ35.170\tA0A140VK53.20\tUPI000049DDFC\tQ9UQ35-1\tNM_016333.4\tNM_016333.4\tP1\t\tdeleterious_low_confidence(0)\tprobably_damaging(0.916)\t11/15\t\tPDB-ENSP_mappings:5mqf.S;PDB-ENSP_mappings:5xjc.U;PDB-ENSP_mappings:5yzg.U;PDB-ENSP_mappings:5z56.U;PDB-ENSP_mappings:5z57.U;PDB-ENSP_mappings:6ff4.S;PDB-ENSP_mappings:6ff7.S;PDB-ENSP_mappings:6icz.U;PANTHER:PTHR34755;PANTHER:PTHR34755:SF3\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t1\tTGCAAGAATGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF174\t7727\tBI\tGRCh38\tchr16\t3402266\t3402266\t+\tMissense_Mutation\tSNP\tC\tC\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.262C>A\tp.Leu88Ile\tp.L88I\tENST00000268655\t1/3\t146\t113\t33\t108\t\t\tZNF174,missense_variant,p.L88I,ENST00000268655,NM_003450.3&NM_001347868.2,c.262C>A,MODERATE,YES,deleterious(0),probably_damaging(0.992),1;ZNF174,missense_variant,p.L88I,ENST00000571936,,c.262C>A,MODERATE,,deleterious(0),probably_damaging(0.992),1;ZNF174,missense_variant,p.L88I,ENST00000344823,NM_001032292.2,c.262C>A,MODERATE,,deleterious(0),probably_damaging(0.996),1;ZNF174,missense_variant,p.L88I,ENST00000575752,,c.262C>A,MODERATE,,deleterious(0),probably_damaging(0.996),1;ZNF174,missense_variant,p.L88I,ENST00000572544,NM_001347869.2&NM_001347870.2,c.262C>A,MODERATE,,deleterious(0),probably_damaging(0.947),1;ZSCAN32,upstream_gene_variant,,ENST00000304926,NM_017810.4&NM_001324345.2&NM_001324341.2&NM_001324344.2&NM_001324342.2&NM_001324340.2,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000396846,,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000396852,NM_001324343.2&NM_001324346.2&NM_001284527.2,,MODIFIER,YES,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000422427,,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000439568,NM_001284529.2,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000571906,,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000573719,,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000573830,,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000574940,,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000618425,NM_001284528.1,,MODIFIER,,,,-1;AC025283.2,intron_variant,,ENST00000575785,,c.-12-2160C>A,MODIFIER,YES,,,1;ZSCAN32,upstream_gene_variant,,ENST00000574084,,,MODIFIER,,,,-1;ZSCAN32,upstream_gene_variant,,ENST00000576500,,,MODIFIER,,,,-1\tA\tENSG00000103343\tENST00000268655\tTranscript\tmissense_variant\tmissense_variant\t1052/2459\t262/1224\t88/407\tL/I\tCtt/Att\tCOSV99237716\t\t1\tZNF174\tHGNC\tHGNC:12963\tprotein_coding\tYES\tCCDS10504.1\tENSP00000268655\tQ15697.192\t\tUPI000013C309\tQ15697-1\tNM_003450.3;NM_001347868.2\tNM_003450.3\tP1\t\tdeleterious(0)\tprobably_damaging(0.992)\t1/3\t\tPDB-ENSP_mappings:1y7q.A;PDB-ENSP_mappings:1y7q.B;PROSITE_profiles:PS50804;CDD:cd07936;PANTHER:PTHR23226:SF175;PANTHER:PTHR23226;Gene3D:1.10.4020.10;Pfam:PF02023;SMART:SM00431;Superfamily:SSF47353\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tTGGAGCTTCTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNMRAL1\t57407\tBI\tGRCh38\tchr16\t4469346\t4469346\t+\tMissense_Mutation\tSNP\tC\tC\tT\trs1177781107\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.160G>A\tp.Val54Ile\tp.V54I\tENST00000283429\t3/6\t334\t261\t73\t270\t\t\tNMRAL1,missense_variant,p.V54I,ENST00000574733,NM_001351994.1,c.160G>A,MODERATE,YES,deleterious(0.04),benign(0.005),-1;NMRAL1,missense_variant,p.V54I,ENST00000574425,,c.160G>A,MODERATE,,deleterious(0.04),benign(0.005),-1;NMRAL1,missense_variant,p.V54I,ENST00000404295,NM_001305142.3&NM_001351996.2&NM_001305141.3,c.160G>A,MODERATE,,deleterious(0.04),benign(0.005),-1;NMRAL1,missense_variant,p.V54I,ENST00000283429,NM_020677.6,c.160G>A,MODERATE,,deleterious(0.04),benign(0.005),-1;NMRAL1,missense_variant,p.V85I,ENST00000573571,,c.253G>A,MODERATE,,tolerated(0.1),benign(0.073),-1;NMRAL1,missense_variant,p.V8I,ENST00000576176,,c.22G>A,MODERATE,,deleterious(0.04),benign(0.104),-1;NMRAL1,upstream_gene_variant,,ENST00000572110,,,MODIFIER,,,,-1;NMRAL1,upstream_gene_variant,,ENST00000572232,NM_001351995.2,,MODIFIER,,,,-1;NMRAL1,non_coding_transcript_exon_variant,,ENST00000575002,,n.266G>A,MODIFIER,,,,-1;NMRAL1,intron_variant,,ENST00000572391,,n.182+158G>A,MODIFIER,,,,-1;NMRAL1,downstream_gene_variant,,ENST00000575557,,,MODIFIER,,,,-1;NMRAL1,downstream_gene_variant,,ENST00000575995,,,MODIFIER,,,,-1;NMRAL1,downstream_gene_variant,,ENST00000576935,,,MODIFIER,,,,-1;NMRAL1,3_prime_UTR_variant,,ENST00000573520,,c.*122G>A,MODIFIER,,,,-1;NMRAL1,intron_variant,,ENST00000571291,,c.*109+158G>A,MODIFIER,,,,-1;NMRAL1,upstream_gene_variant,,ENST00000571448,,,MODIFIER,,,,-1\tT\tENSG00000153406\tENST00000283429\tTranscript\tmissense_variant\tmissense_variant\t266/1092\t160/900\t54/299\tV/I\tGta/Ata\trs1177781107;COSV99361930\t\t-1\tNMRAL1\tHGNC\tHGNC:24987\tprotein_coding\t\tCCDS10516.1\tENSP00000283429\tQ9HBL8.142\tA0A384P622.8\tUPI000007018F\t\tNM_020677.6\tNM_020677.6\tP1\t\tdeleterious(0.04)\tbenign(0.005)\t3/6\t\tPDB-ENSP_mappings:2exx.A;PDB-ENSP_mappings:2exx.B;PDB-ENSP_mappings:2wm3.A;PDB-ENSP_mappings:2wmd.A;PDB-ENSP_mappings:3dxf.A;PDB-ENSP_mappings:3dxf.B;PDB-ENSP_mappings:3e5m.A;PDB-ENSP_mappings:3e5m.B;CDD:cd08947;PANTHER:PTHR42748;PANTHER:PTHR42748:SF16;Gene3D:3.40.50.720;Pfam:PF05368;Superfamily:SSF51735\t\t\t\t\t\t\t\t\t3.976e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.79e-06\t0.0\t0.0\t8.79e-06\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t0;1\t\tCACTACTTCTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSMG1\t23049\tBI\tGRCh38\tchr16\t18838064\t18838064\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.7363G>C\tp.Glu2455Gln\tp.E2455Q\tENST00000446231\t45/63\t56\t48\t8\t58\t\t\tSMG1,missense_variant,p.E2455Q,ENST00000446231,NM_015092.5,c.7363G>C,MODERATE,YES,deleterious(0),probably_damaging(0.979),-1;SMG1,missense_variant,p.E2345Q,ENST00000565324,,c.7033G>C,MODERATE,,deleterious(0),probably_damaging(0.999),-1;SMG1,downstream_gene_variant,,ENST00000563448,,,MODIFIER,,,,-1\tG\tENSG00000157106\tENST00000446231\tTranscript\tmissense_variant\tmissense_variant\t7730/16062\t7363/10986\t2455/3661\tE/Q\tGag/Cag\tCOSV101246805;COSV101246844\t\t-1\tSMG1\tHGNC\tHGNC:30045\tprotein_coding\tYES\tCCDS45430.1\tENSP00000402515\tQ96Q15.169\t\tUPI00004F8E22\tQ96Q15-1\tNM_015092.5\tNM_015092.5\tP1\t\tdeleterious(0)\tprobably_damaging(0.979)\t45/63\t\tGene3D:1.10.1070.11;PDB-ENSP_mappings:6l53.A;PDB-ENSP_mappings:6l54.A;PDB-ENSP_mappings:6syt.A;PROSITE_profiles:PS50290;PANTHER:PTHR11139;PANTHER:PTHR11139:SF71;SMART:SM00146\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1;1\t\tTCGCTCCATCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nDCTN5\t84516\tBI\tGRCh38\tchr16\t23667079\t23667079\t+\tNonsense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.484C>T\tp.Gln162Ter\tp.Q162*\tENST00000300087\t6/6\t99\t82\t17\t82\t\t\tDCTN5,stop_gained,p.Q162*,ENST00000300087,NM_032486.4,c.484C>T,HIGH,YES,,,1;DCTN5,3_prime_UTR_variant,,ENST00000563998,NM_001199743.2,c.*55C>T,MODIFIER,,,,1;DCTN5,downstream_gene_variant,,ENST00000566298,,,MODIFIER,,,,1;DCTN5,downstream_gene_variant,,ENST00000568589,,,MODIFIER,,,,1;DCTN5,3_prime_UTR_variant,,ENST00000566053,,c.*203C>T,MODIFIER,,,,1;DCTN5,non_coding_transcript_exon_variant,,ENST00000563614,,n.612C>T,MODIFIER,,,,1;DCTN5,downstream_gene_variant,,ENST00000563188,,,MODIFIER,,,,1;AC008870.1,upstream_gene_variant,,ENST00000566996,,,MODIFIER,YES,,,1\tT\tENSG00000166847\tENST00000300087\tTranscript\tstop_gained\tstop_gained\t561/10954\t484/549\t162/182\tQ/*\tCag/Tag\tCOSV100266077\t\t1\tDCTN5\tHGNC\tHGNC:24594\tprotein_coding\tYES\tCCDS10615.1\tENSP00000300087\tQ9BTE1.143\t\tUPI0000049C1E\tQ9BTE1-1\tNM_032486.4\tNM_032486.4\tP1\t\t\t\t6/6\t\tPDB-ENSP_mappings:5nw4.h;CDD:cd03359;PANTHER:PTHR46126:SF2;PANTHER:PTHR46126;Gene3D:2.160.10.10;Superfamily:SSF51161\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tHIGH\t1\tSNV\t1\t\t1\t\tGCACTCAGGAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF668\t79759\tBI\tGRCh38\tchr16\t31063935\t31063935\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.525G>C\tp.Lys175Asn\tp.K175N\tENST00000394983\t2/3\t25\t17\t8\t26\t\t\tZNF668,missense_variant,p.K175N,ENST00000538906,NM_001172668.1,c.525G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;ZNF668,missense_variant,p.K175N,ENST00000394983,,c.525G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;ZNF668,missense_variant,p.K175N,ENST00000300849,NM_024706.5,c.525G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;ZNF668,missense_variant,p.K198N,ENST00000539836,NM_001172669.1,c.594G>C,MODERATE,YES,deleterious(0.04),probably_damaging(0.999),-1;ZNF668,missense_variant,p.K175N,ENST00000535577,NM_001172670.1,c.525G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;ZNF668,missense_variant,p.K198N,ENST00000426488,,c.594G>C,MODERATE,,deleterious(0.04),probably_damaging(0.999),-1;ZNF668,intron_variant,,ENST00000414399,,c.165+360G>C,MODIFIER,,,,-1;ZNF668,downstream_gene_variant,,ENST00000417935,,,MODIFIER,,,,-1;ZNF668,downstream_gene_variant,,ENST00000442862,,,MODIFIER,,,,-1;ZNF668,downstream_gene_variant,,ENST00000564456,,,MODIFIER,,,,-1;AC135050.1,downstream_gene_variant,,ENST00000417110,,,MODIFIER,,,,1;AC135050.4,upstream_gene_variant,,ENST00000568708,,,MODIFIER,YES,,,1;AC135050.1,downstream_gene_variant,,ENST00000622229,,,MODIFIER,YES,,,1\tG\tENSG00000167394\tENST00000394983\tTranscript\tmissense_variant\tmissense_variant\t1164/2717\t525/1860\t175/619\tK/N\taaG/aaC\tCOSV100336907\t\t-1\tZNF668\tHGNC\tHGNC:25821\tprotein_coding\t\tCCDS10701.1\tENSP00000378434\tQ96K58.152\tA0A024QZD9.40\tUPI0000E265EB\t\t\t\tP1\t\tdeleterious(0)\tprobably_damaging(1)\t2/3\t\tGene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24376;PANTHER:PTHR24376:SF70;SMART:SM00355;Superfamily:SSF57667\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t5\t\t1\t\tAAGCTCTTGCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nARMC5\t79798\tBI\tGRCh38\tchr16\t31462580\t31462580\t+\tNonsense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1033C>T\tp.Gln345Ter\tp.Q345*\tENST00000268314\t3/6\t82\t58\t24\t70\t\t\tARMC5,stop_gained,p.Q345*,ENST00000457010,NM_024742.2,c.1033C>T,HIGH,,,,1;ARMC5,stop_gained,p.Q440*,ENST00000408912,NM_001288767.2,c.1318C>T,HIGH,YES,,,1;ARMC5,stop_gained,p.Q345*,ENST00000563544,NM_001301820.1,c.1033C>T,HIGH,,,,1;ARMC5,stop_gained,p.Q345*,ENST00000268314,NM_001105247.2,c.1033C>T,HIGH,,,,1;ARMC5,intron_variant,,ENST00000564900,,c.213-192C>T,MODIFIER,,,,1;ARMC5,downstream_gene_variant,,ENST00000564514,,,MODIFIER,,,,1;ARMC5,upstream_gene_variant,,ENST00000570119,,,MODIFIER,,,,1;AC026471.1,upstream_gene_variant,,ENST00000564629,,,MODIFIER,YES,,,-1\tT\tENSG00000140691\tENST00000268314\tTranscript\tstop_gained\tstop_gained\t1057/3108\t1033/2808\t345/935\tQ/*\tCag/Tag\tCOSV99192827\t\t1\tARMC5\tHGNC\tHGNC:25781\tprotein_coding\t\tCCDS45472.1\tENSP00000268314\tQ96C12.144\t\tUPI0000F6E6C0\tQ96C12-1\tNM_001105247.2\tNM_001105247.2\tP4\t\t\t\t3/6\t\tGene3D:1.25.10.10;PANTHER:PTHR23312;SMART:SM00185;Superfamily:SSF48371\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tHIGH\t\tSNV\t5\t\t1\t1\tCCTCCCAGCAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nKIFC3\t3801\tBI\tGRCh38\tchr16\t57762216\t57762216\t+\tMissense_Mutation\tSNP\tC\tC\tT\trs782599223\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1672G>A\tp.Glu558Lys\tp.E558K\tENST00000379655\t13/19\t16\t4\t12\t31\t\t\tKIFC3,missense_variant,p.E558K,ENST00000379655,NM_005550.4,c.1672G>A,MODERATE,,deleterious(0),possibly_damaging(0.659),-1;KIFC3,missense_variant,p.E558K,ENST00000445690,NM_001130100.2,c.1672G>A,MODERATE,,deleterious(0),possibly_damaging(0.659),-1;KIFC3,missense_variant,p.E419K,ENST00000465878,NM_001318715.2,c.1255G>A,MODERATE,,deleterious(0),possibly_damaging(0.555),-1;KIFC3,missense_variant,p.E419K,ENST00000562903,NM_001318714.1,c.1255G>A,MODERATE,,deleterious(0),possibly_damaging(0.555),-1;KIFC3,missense_variant,p.E419K,ENST00000421376,NM_001130099.1,c.1255G>A,MODERATE,,deleterious(0),possibly_damaging(0.555),-1;KIFC3,missense_variant,p.E580K,ENST00000541240,NM_001318710.2,c.1738G>A,MODERATE,YES,deleterious(0.01),possibly_damaging(0.659),-1;KIFC3,missense_variant,p.E416K,ENST00000543930,NM_001318713.1,c.1246G>A,MODERATE,,deleterious(0),benign(0.306),-1;KIFC3,missense_variant,p.E456K,ENST00000540079,NM_001318711.2&NM_001318712.2,c.1366G>A,MODERATE,,deleterious(0),benign(0.027),-1;KIFC3,missense_variant,p.E21K,ENST00000565270,,c.61G>A,MODERATE,,tolerated(0.15),possibly_damaging(0.659),-1;KATNB1,downstream_gene_variant,,ENST00000379661,NM_005886.3,,MODIFIER,YES,,,1;KIFC3,upstream_gene_variant,,ENST00000565397,,,MODIFIER,,,,-1;KIFC3,non_coding_transcript_exon_variant,,ENST00000563266,,n.547G>A,MODIFIER,,,,-1;KIFC3,missense_variant,p.E419K,ENST00000564136,,c.1255G>A,MODERATE,,deleterious(0),benign(0.301),-1;KIFC3,upstream_gene_variant,,ENST00000565753,,,MODIFIER,,,,-1;AC092118.2,downstream_gene_variant,,ENST00000613495,,,MODIFIER,YES,,,1\tT\tENSG00000140859\tENST00000379655\tTranscript\tmissense_variant\tmissense_variant\t1930/3427\t1672/2502\t558/833\tE/K\tGag/Aag\trs782599223;COSV101109098\t\t-1\tKIFC3\tHGNC\tHGNC:6326\tprotein_coding\t\tCCDS10789.2\tENSP00000368976\tQ9BVG8.176\t\tUPI000059D399\tQ9BVG8-3\tNM_005550.4\t\tP4\t\tdeleterious(0)\tpossibly_damaging(0.659)\t13/19\t\tPDB-ENSP_mappings:5wde.A;CDD:cd01366;Gene3D:3.40.850.10;Pfam:PF00225;SMART:SM00129;Superfamily:SSF52540;PROSITE_profiles:PS50067;PANTHER:PTHR24115;PANTHER:PTHR24115:SF387\t\t\t\t\t\t\t\t\t4.225e-06\t0.0\t2.999e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t2.999e-05\tgnomAD_AMR\t2.704379949136637e-05\t0.0\t0.0\t0.0002649360103532672\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0002649360103532672\tamr\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t0;1\t\tCACCTCGGAGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nMEAK7\t57707\tBI\tGRCh38\tchr16\t84486921\t84486921\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs199722035\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.668C>T\tp.Ser223Leu\tp.S223L\tENST00000343629\t5/8\t83\t28\t55\t65\t\t\tMEAK7,missense_variant,p.S223L,ENST00000343629,NM_020947.4,c.668C>T,MODERATE,YES,tolerated(0.18),benign(0.007),-1;MEAK7,downstream_gene_variant,,ENST00000565079,,,MODIFIER,,,,-1;MEAK7,downstream_gene_variant,,ENST00000561807,,,MODIFIER,,,,-1;MEAK7,3_prime_UTR_variant,,ENST00000566995,,c.*82C>T,MODIFIER,,,,-1;MEAK7,3_prime_UTR_variant,,ENST00000570036,,c.*723C>T,MODIFIER,,,,-1;MEAK7,non_coding_transcript_exon_variant,,ENST00000567321,,n.1516C>T,MODIFIER,,,,-1\tA\tENSG00000140950\tENST00000343629\tTranscript\tmissense_variant\tmissense_variant\t752/5013\t668/1371\t223/456\tS/L\ttCg/tTg\trs199722035\t\t-1\tMEAK7\tHGNC\tHGNC:29325\tprotein_coding\tYES\tCCDS32498.1\tENSP00000343635\tQ6P9B6.125\t\tUPI00001BBB2E\t\tNM_020947.4\tNM_020947.4\tP1\t\ttolerated(0.18)\tbenign(0.007)\t5/8\t\tPANTHER:PTHR23354;PANTHER:PTHR23354:SF97\t0.0002\t0.0\t0.0\t0.001\t0.0\t0.0\t0.0002273\t0.0\t6.367e-05\t6.157e-05\t2.892e-05\t0.0\t0.0002718\t0.0001386\t3.521e-05\t0.0\t6.533e-05\t0.001\tEAS\t7.436949817929417e-05\t9.731409954838455e-05\t0.0\t0.0\t0.0\t0.0008071030024439096\t0.0001882880023913458\t0.0\t0.0\t0.0004965239786542952\t0.0\t0.0008071030024439096\teas\t\t\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t\t\tGAGACGAGCAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nRPL13\t6137\tBI\tGRCh38\tchr16\t89560974\t89560974\t+\tSilent\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.15G>C\tp.Arg5=\tp.R5=\tENST00000311528\t2/6\t32\t13\t19\t25\t\t\tRPL13,synonymous_variant,p.R5=,ENST00000393099,NM_033251.2,c.15G>C,LOW,YES,,,1;RPL13,synonymous_variant,p.R5=,ENST00000311528,NM_000977.4,c.15G>C,LOW,,,,1;RPL13,synonymous_variant,p.R5=,ENST00000452368,NM_001243131.1,c.15G>C,LOW,,,,1;RPL13,synonymous_variant,p.R5=,ENST00000567815,,c.15G>C,LOW,,,,1;RPL13,synonymous_variant,p.R5=,ENST00000467736,,c.15G>C,LOW,,,,1;RPL13,intron_variant,,ENST00000563270,,c.-358-253G>C,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000268704,,,MODIFIER,,,,1;RPL13,upstream_gene_variant,,ENST00000472354,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000565891,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643649,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644671,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644781,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645063,NM_001363850.1,,MODIFIER,YES,,,1;SPG7,downstream_gene_variant,,ENST00000645818,NM_003119.4,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645897,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646303,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646445,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646716,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000647032,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000647079,,,MODIFIER,,,,1;SNORD68,upstream_gene_variant,,ENST00000363214,,,MODIFIER,YES,,,1;SPG7,downstream_gene_variant,,ENST00000643350,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643496,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645742,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645842,,,MODIFIER,,,,1;RPL13,synonymous_variant,p.R5=,ENST00000562879,,c.15G>C,LOW,,,,1;RPL13,non_coding_transcript_exon_variant,,ENST00000563749,,n.298G>C,MODIFIER,,,,1;RPL13,non_coding_transcript_exon_variant,,ENST00000484610,,n.69G>C,MODIFIER,,,,1;RPL13,non_coding_transcript_exon_variant,,ENST00000399461,,n.71G>C,MODIFIER,,,,1;RPL13,non_coding_transcript_exon_variant,,ENST00000491523,,n.71G>C,MODIFIER,,,,1;RPL13,non_coding_transcript_exon_variant,,ENST00000487034,,n.66G>C,MODIFIER,,,,1;RPL13,non_coding_transcript_exon_variant,,ENST00000565571,,n.65G>C,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000561702,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000561911,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000569720,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000569820,,,MODIFIER,,,,1;RPL13,upstream_gene_variant,,ENST00000570149,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000642226,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000642334,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000642814,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000642984,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643105,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643409,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643668,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643724,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000643954,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644171,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644210,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644225,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644281,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644464,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644498,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644751,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000644901,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645042,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645392,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645886,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645952,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000645977,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646005,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646263,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646399,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646531,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646589,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646826,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000646930,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000647123,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000647227,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000647302,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000647476,,,MODIFIER,,,,1;SPG7,downstream_gene_variant,,ENST00000647491,,,MODIFIER,,,,1\tC\tENSG00000167526\tENST00000311528\tTranscript\tsynonymous_variant\tsynonymous_variant\t66/2187\t15/636\t5/211\tR\tcgG/cgC\tCOSV99245374;COSV99245426\t\t1\tRPL13\tHGNC\tHGNC:10303\tprotein_coding\t\tCCDS10979.1\tENSP00000307889\tP26373.197\tA8K4C8.110\tUPI0000001228\tP26373-1\tNM_000977.4\tNM_000977.4\tP1\t\t\t\t2/6\t\tPDB-ENSP_mappings:4ug0.LL;PDB-ENSP_mappings:4v6x.CL;PDB-ENSP_mappings:5aj0.AL;PDB-ENSP_mappings:5lks.LL;PDB-ENSP_mappings:5t2c.r;PDB-ENSP_mappings:6ek0.LL;PDB-ENSP_mappings:6ip5.2F;PDB-ENSP_mappings:6ip6.2F;PDB-ENSP_mappings:6ip8.2F;PDB-ENSP_mappings:6ole.M;PDB-ENSP_mappings:6olf.M;PDB-ENSP_mappings:6olg.AL;PDB-ENSP_mappings:6oli.M;PDB-ENSP_mappings:6olz.AL;PDB-ENSP_mappings:6om0.M;PDB-ENSP_mappings:6om7.M;PDB-ENSP_mappings:6qzp.LL;PDB-ENSP_mappings:6y0g.LL;PDB-ENSP_mappings:6y2l.LL;PDB-ENSP_mappings:6y57.LL;PANTHER:PTHR11722:SF4;PANTHER:PTHR11722\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t1;1\t1\tAGCCGGAATGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nRPA1\t6117\tBI\tGRCh38\tchr17\t1843992\t1843992\t+\tSilent\tSNP\tC\tC\tT\tnovel\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.157C>T\tp.Leu53=\tp.L53=\tENST00000254719\t3/17\t72\t61\t11\t52\t\t\tRPA1,synonymous_variant,p.L53=,ENST00000254719,NM_001355120.2&NM_002945.5&NM_001355121.2,c.157C>T,LOW,YES,,,1;RPA1,synonymous_variant,p.L40=,ENST00000570451,,c.118C>T,LOW,,,,1;RPA1,synonymous_variant,p.L40=,ENST00000571058,,c.118C>T,LOW,,,,1;RPA1,non_coding_transcript_exon_variant,,ENST00000571725,,n.73C>T,MODIFIER,,,,1\tT\tENSG00000132383\tENST00000254719\tTranscript\tsynonymous_variant\tsynonymous_variant\t246/4847\t157/1851\t53/616\tL\tCta/Tta\t\t\t1\tRPA1\tHGNC\tHGNC:10289\tprotein_coding\tYES\tCCDS11014.1\tENSP00000254719\tP27694.215\t\tUPI000013379A\t\tNM_001355120.2;NM_002945.5;NM_001355121.2\tNM_002945.5\tP1\t\t\t\t3/17\t\tPDB-ENSP_mappings:1ewi.A;Gene3D:2.40.50.140;PDB-ENSP_mappings:2b29.A;PDB-ENSP_mappings:2b3g.A;PDB-ENSP_mappings:4ijh.A;PDB-ENSP_mappings:4ijl.A;PDB-ENSP_mappings:4ipc.A;PDB-ENSP_mappings:4ipd.A;PDB-ENSP_mappings:4ipg.A;PDB-ENSP_mappings:4iph.A;PDB-ENSP_mappings:4luo.A;PDB-ENSP_mappings:4luv.A;PDB-ENSP_mappings:4luz.A;PDB-ENSP_mappings:4lw1.A;PDB-ENSP_mappings:4lwc.A;PDB-ENSP_mappings:4nb3.A;PDB-ENSP_mappings:4nb3.B;PDB-ENSP_mappings:4o0a.A;PDB-ENSP_mappings:4r4c.A;PDB-ENSP_mappings:4r4i.A;PDB-ENSP_mappings:4r4o.A;PDB-ENSP_mappings:4r4q.A;PDB-ENSP_mappings:4r4t.A;PDB-ENSP_mappings:5e7n.A;PDB-ENSP_mappings:5eay.A;PDB-ENSP_mappings:5eay.B;PDB-ENSP_mappings:5eay.C;PDB-ENSP_mappings:5eay.D;PDB-ENSP_mappings:5n85.A;PDB-ENSP_mappings:5n8a.A;Pfam:PF04057;PANTHER:PTHR23273;PANTHER:PTHR23273:SF4;Superfamily:SSF50249;TIGRFAM:TIGR00617;CDD:cd04477\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t\t\tACACTCTATCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nRPA1\t6117\tBI\tGRCh38\tchr17\t1844607\t1844607\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.193C>T\tp.Leu65Phe\tp.L65F\tENST00000254719\t4/17\t33\t26\t7\t22\t\t\tRPA1,missense_variant,p.L65F,ENST00000254719,NM_001355120.2&NM_002945.5&NM_001355121.2,c.193C>T,MODERATE,YES,tolerated(0.06),probably_damaging(0.959),1;RPA1,missense_variant,p.L52F,ENST00000570451,,c.154C>T,MODERATE,,deleterious(0),probably_damaging(0.959),1;RPA1,missense_variant,p.L52F,ENST00000571058,,c.154C>T,MODERATE,,tolerated(0.05),probably_damaging(0.959),1;RPA1,non_coding_transcript_exon_variant,,ENST00000571725,,n.109C>T,MODIFIER,,,,1\tT\tENSG00000132383\tENST00000254719\tTranscript\tmissense_variant\tmissense_variant\t282/4847\t193/1851\t65/616\tL/F\tCtc/Ttc\tCOSV99628365\t\t1\tRPA1\tHGNC\tHGNC:10289\tprotein_coding\tYES\tCCDS11014.1\tENSP00000254719\tP27694.215\t\tUPI000013379A\t\tNM_001355120.2;NM_002945.5;NM_001355121.2\tNM_002945.5\tP1\t\ttolerated(0.06)\tprobably_damaging(0.959)\t4/17\t\tPDB-ENSP_mappings:1ewi.A;Gene3D:2.40.50.140;PDB-ENSP_mappings:2b29.A;PDB-ENSP_mappings:2b3g.A;PDB-ENSP_mappings:4ijh.A;PDB-ENSP_mappings:4ijl.A;PDB-ENSP_mappings:4ipc.A;PDB-ENSP_mappings:4ipd.A;PDB-ENSP_mappings:4ipg.A;PDB-ENSP_mappings:4iph.A;PDB-ENSP_mappings:4luo.A;PDB-ENSP_mappings:4luv.A;PDB-ENSP_mappings:4luz.A;PDB-ENSP_mappings:4lw1.A;PDB-ENSP_mappings:4lwc.A;PDB-ENSP_mappings:4nb3.A;PDB-ENSP_mappings:4nb3.B;PDB-ENSP_mappings:4o0a.A;PDB-ENSP_mappings:4r4c.A;PDB-ENSP_mappings:4r4i.A;PDB-ENSP_mappings:4r4o.A;PDB-ENSP_mappings:4r4q.A;PDB-ENSP_mappings:4r4t.A;PDB-ENSP_mappings:5e7n.A;PDB-ENSP_mappings:5eay.A;PDB-ENSP_mappings:5eay.B;PDB-ENSP_mappings:5eay.C;PDB-ENSP_mappings:5eay.D;PDB-ENSP_mappings:5n85.A;PDB-ENSP_mappings:5n8a.A;Pfam:PF04057;PANTHER:PTHR23273;PANTHER:PTHR23273:SF4;Superfamily:SSF50249;TIGRFAM:TIGR00617;CDD:cd04477\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tACCCTCTCGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTRPV3\t162514\tBI\tGRCh38\tchr17\t3518833\t3518833\t+\tMissense_Mutation\tSNP\tC\tC\tT\trs148302879\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1828G>A\tp.Glu610Lys\tp.E610K\tENST00000576742\t15/18\t33\t25\t8\t34\t\t\tTRPV3,missense_variant,p.E610K,ENST00000576742,NM_145068.4,c.1828G>A,MODERATE,,tolerated(0.25),probably_damaging(0.94),-1;TRPV3,missense_variant,p.E594K,ENST00000616411,,c.1780G>A,MODERATE,,tolerated(0.25),benign(0.057),-1;TRPV3,missense_variant,p.E610K,ENST00000301365,NM_001258205.2,c.1828G>A,MODERATE,YES,tolerated(0.25),possibly_damaging(0.9),-1;TRPV3,missense_variant,p.E610K,ENST00000572519,,c.1828G>A,MODERATE,,tolerated(0.21),probably_damaging(0.988),-1;SPATA22,upstream_gene_variant,,ENST00000541913,NM_001321336.1,,MODIFIER,,,,-1;TRPV3,missense_variant,p.R116Q,ENST00000577016,,c.347G>A,MODERATE,,tolerated_low_confidence(0.09),unknown(0),-1;TRPV3,3_prime_UTR_variant,,ENST00000381913,,c.*71G>A,MODIFIER,,,,-1;TRPV3,3_prime_UTR_variant,,ENST00000573539,,c.*1838G>A,MODIFIER,,,,-1;TRPV3,3_prime_UTR_variant,,ENST00000571139,,c.*1820G>A,MODIFIER,,,,-1\tT\tENSG00000167723\tENST00000576742\tTranscript\tmissense_variant\tmissense_variant\t1967/5927\t1828/2373\t610/790\tE/K\tGag/Aag\trs148302879\t\t-1\tTRPV3\tHGNC\tHGNC:18084\tprotein_coding\t\tCCDS11029.1\tENSP00000461518\tQ8NET8.146\t\tUPI000006FF4A\tQ8NET8-1\tNM_145068.4\tNM_145068.4\tA1\t\ttolerated(0.25)\tprobably_damaging(0.94)\t15/18\t\tPDB-ENSP_mappings:6mho.A;PDB-ENSP_mappings:6mho.B;PDB-ENSP_mappings:6mho.C;PDB-ENSP_mappings:6mho.D;PDB-ENSP_mappings:6mhs.A;PDB-ENSP_mappings:6mhs.B;PDB-ENSP_mappings:6mhs.C;PDB-ENSP_mappings:6mhs.D;PDB-ENSP_mappings:6mhv.A;PDB-ENSP_mappings:6mhv.B;PDB-ENSP_mappings:6mhv.C;PDB-ENSP_mappings:6mhv.D;PDB-ENSP_mappings:6mhw.A;PDB-ENSP_mappings:6mhw.B;PDB-ENSP_mappings:6mhw.C;PDB-ENSP_mappings:6mhw.D;PDB-ENSP_mappings:6mhx.A;PDB-ENSP_mappings:6mhx.B;PDB-ENSP_mappings:6mhx.C;PDB-ENSP_mappings:6mhx.D;PDB-ENSP_mappings:6ot2.A;PDB-ENSP_mappings:6ot2.B;PDB-ENSP_mappings:6ot2.C;PDB-ENSP_mappings:6ot2.D;PDB-ENSP_mappings:6ot5.A;PDB-ENSP_mappings:6ot5.B;PDB-ENSP_mappings:6ot5.C;PDB-ENSP_mappings:6ot5.D;Pfam:PF00520;PANTHER:PTHR10582;PANTHER:PTHR10582:SF6\t0.0002\t0.0\t0.0\t0.001\t0.0\t0.0\t0.000227\t0.0\t4.785e-05\t0.0002462\t0.0\t0.0\t5.438e-05\t0.0\t5.298e-05\t0.0001635\t0.0\t0.001\tEAS\t4.731069930130616e-05\t0.00014587200712412596\t0.0\t0.0\t0.0\t0.00020153200603090227\t0.0\t0.0\t0.0\t0.0\t0.0\t0.00014587200712412596\tafr\t\t\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t\t1\tCTTCTCGATCA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nATP2A3\t489\tBI\tGRCh38\tchr17\t3947692\t3947692\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.794C>T\tp.Ser265Phe\tp.S265F\tENST00000352011\t8/22\t53\t36\t17\t56\t\t\tATP2A3,missense_variant,p.S265F,ENST00000309890,NM_174956.2,c.794C>T,MODERATE,,tolerated(0.15),benign(0.031),-1;ATP2A3,missense_variant,p.S265F,ENST00000397041,NM_005173.4,c.794C>T,MODERATE,,tolerated(0.14),benign(0.031),-1;ATP2A3,missense_variant,p.S265F,ENST00000397035,NM_174958.3,c.794C>T,MODERATE,,tolerated(0.15),benign(0.031),-1;ATP2A3,missense_variant,p.S265F,ENST00000359983,NM_174954.3&NM_174953.3,c.794C>T,MODERATE,YES,tolerated(0.17),benign(0.046),-1;ATP2A3,missense_variant,p.S265F,ENST00000352011,NM_174955.3,c.794C>T,MODERATE,,tolerated(0.14),benign(0.049),-1;ATP2A3,missense_variant,p.S265F,ENST00000397043,NM_174957.3,c.794C>T,MODERATE,,tolerated(0.16),benign(0.006),-1;ATP2A3,upstream_gene_variant,,ENST00000572694,,,MODIFIER,,,,-1\tA\tENSG00000074370\tENST00000352011\tTranscript\tmissense_variant\tmissense_variant\t849/3274\t794/3132\t265/1043\tS/F\ttCt/tTt\tCOSV99989660\t\t-1\tATP2A3\tHGNC\tHGNC:813\tprotein_coding\t\tCCDS11041.1\tENSP00000301387\tQ93084.199\t\tUPI00001261E5\tQ93084-1\tNM_174955.3\t\t\t\ttolerated(0.14)\tbenign(0.049)\t8/22\t\tGene3D:1.20.1110.10;Pfam:PF00122;PANTHER:PTHR42861;PANTHER:PTHR42861:SF6;Superfamily:SSF81665;TIGRFAM:TIGR01116;TIGRFAM:TIGR01494;Transmembrane_helices:TMhelix;CDD:cd02083\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t5\t\t1\t\tTCACAGAGATG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTP53\t7157\tBI\tGRCh38\tchr17\t7674953\t7674953\t+\tMissense_Mutation\tSNP\tT\tT\tA\trs786201838\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.578A>T\tp.His193Leu\tp.H193L\tENST00000269305\t6/11\t69\t41\t27\t46\t\t\tTP53,missense_variant,p.H193L,ENST00000420246,,c.578A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H154L,ENST00000622645,NM_001126114.2&NM_001276696.2,c.461A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H154L,ENST00000610292,NM_001126118.1,c.461A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H193L,ENST00000455263,NM_001126113.2&NM_001276695.2,c.578A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H154L,ENST00000610538,,c.461A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H154L,ENST00000620739,,c.461A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H193L,ENST00000269305,NM_000546.6,c.578A>T,MODERATE,YES,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H193L,ENST00000445888,NM_001126112.2&NM_001276761.2&NM_001276760.2,c.578A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H154L,ENST00000619485,,c.461A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H61L,ENST00000510385,NM_001126116.1&NM_001276698.2,c.182A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H34L,ENST00000618944,,c.101A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H61L,ENST00000504290,,c.182A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H34L,ENST00000610623,NM_001126117.1&NM_001276699.2,c.101A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H61L,ENST00000504937,,c.182A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H34L,ENST00000619186,NM_001126115.1&NM_001276697.2,c.101A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H193L,ENST00000359597,,c.578A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H193L,ENST00000413465,,c.578A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H61L,ENST00000509690,,c.182A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,missense_variant,p.H100L,ENST00000514944,,c.299A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,downstream_gene_variant,,ENST00000503591,,,MODIFIER,,,,-1;TP53,downstream_gene_variant,,ENST00000508793,,,MODIFIER,,,,-1;TP53,upstream_gene_variant,,ENST00000576024,,,MODIFIER,,,,-1;TP53,downstream_gene_variant,,ENST00000604348,,,MODIFIER,,,,-1;TP53,intron_variant,,ENST00000574684,,n.67+100A>T,MODIFIER,,,,-1;TP53,missense_variant,p.H154L,ENST00000635293,,c.461A>T,MODERATE,,deleterious(0),probably_damaging(1),-1;TP53,non_coding_transcript_exon_variant,,ENST00000505014,,n.834A>T,MODIFIER,,,,-1\tA\tENSG00000141510\tENST00000269305\tTranscript\tmissense_variant\tmissense_variant\t720/2512\t578/1182\t193/393\tH/L\tcAt/cTt\trs786201838;CM083194;CM951225;COSV52662414;COSV52663304;COSV52681707\t\t-1\tTP53\tHGNC\tHGNC:11998\tprotein_coding\tYES\tCCDS11118.1\tENSP00000269305\tP04637.285\tK7PPA8.70\tUPI000002ED67\tP04637-1\tNM_000546.6\tNM_000546.6\tP1\t\tdeleterious(0)\tprobably_damaging(1)\t6/11\t\tPDB-ENSP_mappings:1gzh.A;PDB-ENSP_mappings:1gzh.C;PDB-ENSP_mappings:1kzy.A;PDB-ENSP_mappings:1kzy.B;PDB-ENSP_mappings:1tsr.A;PDB-ENSP_mappings:1tsr.B;PDB-ENSP_mappings:1tsr.C;PDB-ENSP_mappings:1tup.A;PDB-ENSP_mappings:1tup.B;PDB-ENSP_mappings:1tup.C;PDB-ENSP_mappings:1uol.A;PDB-ENSP_mappings:1uol.B;PDB-ENSP_mappings:1ycs.A;Gene3D:2.60.40.720;PDB-ENSP_mappings:2ac0.A;PDB-ENSP_mappings:2ac0.B;PDB-ENSP_mappings:2ac0.C;PDB-ENSP_mappings:2ac0.D;PDB-ENSP_mappings:2ady.A;PDB-ENSP_mappings:2ady.B;PDB-ENSP_mappings:2ahi.A;PDB-ENSP_mappings:2ahi.B;PDB-ENSP_mappings:2ahi.C;PDB-ENSP_mappings:2ahi.D;PDB-ENSP_mappings:2ata.A;PDB-ENSP_mappings:2ata.B;PDB-ENSP_mappings:2ata.C;PDB-ENSP_mappings:2ata.D;PDB-ENSP_mappings:2bim.A;PDB-ENSP_mappings:2bim.B;PDB-ENSP_mappings:2bin.A;PDB-ENSP_mappings:2bio.A;PDB-ENSP_mappings:2bip.A;PDB-ENSP_mappings:2biq.A;PDB-ENSP_mappings:2fej.A;PDB-ENSP_mappings:2h1l.M;PDB-ENSP_mappings:2h1l.N;PDB-ENSP_mappings:2h1l.O;PDB-ENSP_mappings:2h1l.P;PDB-ENSP_mappings:2h1l.Q;PDB-ENSP_mappings:2h1l.R;PDB-ENSP_mappings:2h1l.S;PDB-ENSP_mappings:2h1l.T;PDB-ENSP_mappings:2h1l.U;PDB-ENSP_mappings:2h1l.V;PDB-ENSP_mappings:2h1l.W;PDB-ENSP_mappings:2h1l.X;PDB-ENSP_mappings:2j1w.A;PDB-ENSP_mappings:2j1w.B;PDB-ENSP_mappings:2j1x.A;PDB-ENSP_mappings:2j1x.B;PDB-ENSP_mappings:2j1y.A;PDB-ENSP_mappings:2j1y.B;PDB-ENSP_mappings:2j1y.C;PDB-ENSP_mappings:2j1y.D;PDB-ENSP_mappings:2j1z.A;PDB-ENSP_mappings:2j1z.B;PDB-ENSP_mappings:2j20.A;PDB-ENSP_mappings:2j20.B;PDB-ENSP_mappings:2j21.A;PDB-ENSP_mappings:2j21.B;PDB-ENSP_mappings:2mej.B;PDB-ENSP_mappings:2ocj.A;PDB-ENSP_mappings:2ocj.B;PDB-ENSP_mappings:2ocj.C;PDB-ENSP_mappings:2ocj.D;PDB-ENSP_mappings:2pcx.A;PDB-ENSP_mappings:2vuk.A;PDB-ENSP_mappings:2vuk.B;PDB-ENSP_mappings:2wgx.A;PDB-ENSP_mappings:2wgx.B;PDB-ENSP_mappings:2x0u.A;PDB-ENSP_mappings:2x0u.B;PDB-ENSP_mappings:2x0v.A;PDB-ENSP_mappings:2x0v.B;PDB-ENSP_mappings:2x0w.A;PDB-ENSP_mappings:2x0w.B;PDB-ENSP_mappings:2xwr.A;PDB-ENSP_mappings:2xwr.B;PDB-ENSP_mappings:2ybg.A;PDB-ENSP_mappings:2ybg.B;PDB-ENSP_mappings:2ybg.C;PDB-ENSP_mappings:2ybg.D;PDB-ENSP_mappings:3d05.A;PDB-ENSP_mappings:3d06.A;PDB-ENSP_mappings:3d07.A;PDB-ENSP_mappings:3d07.B;PDB-ENSP_mappings:3d08.A;PDB-ENSP_mappings:3d09.A;PDB-ENSP_mappings:3d0a.A;PDB-ENSP_mappings:3d0a.B;PDB-ENSP_mappings:3d0a.C;PDB-ENSP_mappings:3d0a.D;PDB-ENSP_mappings:3igk.A;PDB-ENSP_mappings:3igl.A;PDB-ENSP_mappings:3kmd.A;PDB-ENSP_mappings:3kmd.B;PDB-ENSP_mappings:3kmd.C;PDB-ENSP_mappings:3kmd.D;PDB-ENSP_mappings:3kz8.A;PDB-ENSP_mappings:3kz8.B;PDB-ENSP_mappings:3q01.A;PDB-ENSP_mappings:3q01.B;PDB-ENSP_mappings:3q05.A;PDB-ENSP_mappings:3q05.B;PDB-ENSP_mappings:3q05.C;PDB-ENSP_mappings:3q05.D;PDB-ENSP_mappings:3q06.A;PDB-ENSP_mappings:3q06.B;PDB-ENSP_mappings:3q06.C;PDB-ENSP_mappings:3q06.D;PDB-ENSP_mappings:3ts8.A;PDB-ENSP_mappings:3ts8.B;PDB-ENSP_mappings:3ts8.C;PDB-ENSP_mappings:3ts8.D;PDB-ENSP_mappings:3zme.A;PDB-ENSP_mappings:3zme.B;PDB-ENSP_mappings:4agl.A;PDB-ENSP_mappings:4agl.B;PDB-ENSP_mappings:4agm.A;PDB-ENSP_mappings:4agm.B;PDB-ENSP_mappings:4agn.A;PDB-ENSP_mappings:4agn.B;PDB-ENSP_mappings:4ago.A;PDB-ENSP_mappings:4ago.B;PDB-ENSP_mappings:4agp.A;PDB-ENSP_mappings:4agp.B;PDB-ENSP_mappings:4agq.A;PDB-ENSP_mappings:4agq.B;PDB-ENSP_mappings:4hje.A;PDB-ENSP_mappings:4hje.B;PDB-ENSP_mappings:4hje.C;PDB-ENSP_mappings:4hje.D;PDB-ENSP_mappings:4ibq.A;PDB-ENSP_mappings:4ibq.B;PDB-ENSP_mappings:4ibq.C;PDB-ENSP_mappings:4ibq.D;PDB-ENSP_mappings:4ibs.A;PDB-ENSP_mappings:4ibs.B;PDB-ENSP_mappings:4ibs.C;PDB-ENSP_mappings:4ibs.D;PDB-ENSP_mappings:4ibt.A;PDB-ENSP_mappings:4ibt.B;PDB-ENSP_mappings:4ibt.C;PDB-ENSP_mappings:4ibt.D;PDB-ENSP_mappings:4ibu.A;PDB-ENSP_mappings:4ibu.B;PDB-ENSP_mappings:4ibu.C;PDB-ENSP_mappings:4ibu.D;PDB-ENSP_mappings:4ibv.A;PDB-ENSP_mappings:4ibw.A;PDB-ENSP_mappings:4iby.A;PDB-ENSP_mappings:4iby.B;PDB-ENSP_mappings:4ibz.A;PDB-ENSP_mappings:4ibz.B;PDB-ENSP_mappings:4ibz.C;PDB-ENSP_mappings:4ibz.D;PDB-ENSP_mappings:4ijt.A;PDB-ENSP_mappings:4kvp.A;PDB-ENSP_mappings:4kvp.B;PDB-ENSP_mappings:4kvp.C;PDB-ENSP_mappings:4kvp.D;PDB-ENSP_mappings:4lo9.A;PDB-ENSP_mappings:4lo9.B;PDB-ENSP_mappings:4lo9.C;PDB-ENSP_mappings:4lo9.D;PDB-ENSP_mappings:4loe.A;PDB-ENSP_mappings:4loe.B;PDB-ENSP_mappings:4loe.C;PDB-ENSP_mappings:4loe.D;PDB-ENSP_mappings:4lof.A;PDB-ENSP_mappings:4mzi.A;PDB-ENSP_mappings:4mzr.A;PDB-ENSP_mappings:4mzr.B;PDB-ENSP_mappings:4mzr.C;PDB-ENSP_mappings:4mzr.D;PDB-ENSP_mappings:4qo1.B;PDB-ENSP_mappings:4xr8.C;PDB-ENSP_mappings:4xr8.D;PDB-ENSP_mappings:5a7b.A;PDB-ENSP_mappings:5a7b.B;PDB-ENSP_mappings:5ab9.A;PDB-ENSP_mappings:5ab9.B;PDB-ENSP_mappings:5aba.A;PDB-ENSP_mappings:5aba.B;PDB-ENSP_mappings:5aoi.A;PDB-ENSP_mappings:5aoi.B;PDB-ENSP_mappings:5aoj.A;PDB-ENSP_mappings:5aoj.B;PDB-ENSP_mappings:5aok.A;PDB-ENSP_mappings:5aok.B;PDB-ENSP_mappings:5aol.A;PDB-ENSP_mappings:5aol.B;PDB-ENSP_mappings:5aom.A;PDB-ENSP_mappings:5aom.B;PDB-ENSP_mappings:5bua.A;PDB-ENSP_mappings:5ecg.A;PDB-ENSP_mappings:5ecg.B;PDB-ENSP_mappings:5g4m.A;PDB-ENSP_mappings:5g4m.B;PDB-ENSP_mappings:5g4n.A;PDB-ENSP_mappings:5g4n.B;PDB-ENSP_mappings:5g4o.A;PDB-ENSP_mappings:5g4o.B;PDB-ENSP_mappings:5lap.A;PDB-ENSP_mappings:5lap.B;PDB-ENSP_mappings:5lgy.A;PDB-ENSP_mappings:5lgy.B;PDB-ENSP_mappings:5lgy.C;PDB-ENSP_mappings:5lgy.D;PDB-ENSP_mappings:5mct.A;PDB-ENSP_mappings:5mct.B;PDB-ENSP_mappings:5mcu.A;PDB-ENSP_mappings:5mcu.B;PDB-ENSP_mappings:5mcv.A;PDB-ENSP_mappings:5mcv.B;PDB-ENSP_mappings:5mcw.A;PDB-ENSP_mappings:5mcw.B;PDB-ENSP_mappings:5mf7.A;PDB-ENSP_mappings:5mf7.B;PDB-ENSP_mappings:5mg7.A;PDB-ENSP_mappings:5mg7.B;PDB-ENSP_mappings:5o1a.A;PDB-ENSP_mappings:5o1a.B;PDB-ENSP_mappings:5o1b.A;PDB-ENSP_mappings:5o1b.B;PDB-ENSP_mappings:5o1c.A;PDB-ENSP_mappings:5o1c.B;PDB-ENSP_mappings:5o1d.A;PDB-ENSP_mappings:5o1d.B;PDB-ENSP_mappings:5o1e.A;PDB-ENSP_mappings:5o1e.B;PDB-ENSP_mappings:5o1f.A;PDB-ENSP_mappings:5o1f.B;PDB-ENSP_mappings:5o1g.A;PDB-ENSP_mappings:5o1g.B;PDB-ENSP_mappings:5o1h.A;PDB-ENSP_mappings:5o1h.B;PDB-ENSP_mappings:5o1i.A;PDB-ENSP_mappings:5o1i.B;PDB-ENSP_mappings:5xzc.B;PDB-ENSP_mappings:5xzc.C;PDB-ENSP_mappings:5xzc.D;PDB-ENSP_mappings:5xzc.E;PDB-ENSP_mappings:6ff9.A;PDB-ENSP_mappings:6ff9.B;PDB-ENSP_mappings:6ff9.C;PDB-ENSP_mappings:6ff9.D;PDB-ENSP_mappings:6fj5.A;PDB-ENSP_mappings:6fj5.B;PDB-ENSP_mappings:6fj5.C;PDB-ENSP_mappings:6fj5.D;PDB-ENSP_mappings:6gga.A;PDB-ENSP_mappings:6gga.B;PDB-ENSP_mappings:6ggb.A;PDB-ENSP_mappings:6ggb.B;PDB-ENSP_mappings:6ggc.A;PDB-ENSP_mappings:6ggc.B;PDB-ENSP_mappings:6ggd.A;PDB-ENSP_mappings:6ggd.B;PDB-ENSP_mappings:6gge.A;PDB-ENSP_mappings:6gge.B;PDB-ENSP_mappings:6ggf.A;PDB-ENSP_mappings:6ggf.B;PDB-ENSP_mappings:6rz3.A;PDB-ENSP_mappings:6shz.A;PDB-ENSP_mappings:6shz.B;PDB-ENSP_mappings:6si0.A;PDB-ENSP_mappings:6si0.B;PDB-ENSP_mappings:6si1.A;PDB-ENSP_mappings:6si1.B;PDB-ENSP_mappings:6si2.A;PDB-ENSP_mappings:6si2.B;PDB-ENSP_mappings:6si3.A;PDB-ENSP_mappings:6si3.B;PDB-ENSP_mappings:6si4.A;PDB-ENSP_mappings:6si4.B;PDB-ENSP_mappings:6sl6.A;Pfam:PF00870;PANTHER:PTHR11447;PANTHER:PTHR11447:SF6;Superfamily:SSF49417;CDD:cd08367\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tlikely_pathogenic;uncertain_significance\t0;0;0;1;1;1\t26619011\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1;1;1;1;1;1\t1\tTAAGATGCTGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM11066;COSM2744772;COSM3732881;COSM99916;COSM99917;COSM99918;COSM99919\tY\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTP53\t7157\tBI\tGRCh38\tchr17\t7675145\t7675146\t+\tFrame_Shift_Ins\tINS\t-\t-\tGGGT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.463_466dup\tp.Arg156HisfsTer26\tp.R156Hfs*26\tENST00000269305\t5/11\t77\t65\t12\t77\t\t\tTP53,frameshift_variant,p.R156Hfs*26,ENST00000420246,,c.463_466dup,HIGH,,,,-1;TP53,frameshift_variant,p.R117Hfs*26,ENST00000622645,NM_001126114.2&NM_001276696.2,c.346_349dup,HIGH,,,,-1;TP53,frameshift_variant,p.R117Hfs*26,ENST00000610292,NM_001126118.1,c.346_349dup,HIGH,,,,-1;TP53,frameshift_variant,p.R156Hfs*26,ENST00000455263,NM_001126113.2&NM_001276695.2,c.463_466dup,HIGH,,,,-1;TP53,frameshift_variant,p.R117Hfs*26,ENST00000610538,,c.346_349dup,HIGH,,,,-1;TP53,frameshift_variant,p.R117Hfs*26,ENST00000620739,,c.346_349dup,HIGH,,,,-1;TP53,frameshift_variant,p.R156Hfs*26,ENST00000269305,NM_000546.6,c.463_466dup,HIGH,YES,,,-1;TP53,frameshift_variant,p.R156Hfs*26,ENST00000445888,NM_001126112.2&NM_001276761.2&NM_001276760.2,c.463_466dup,HIGH,,,,-1;TP53,frameshift_variant,p.R117Hfs*26,ENST00000619485,,c.346_349dup,HIGH,,,,-1;TP53,frameshift_variant,p.R24Hfs*26,ENST00000510385,NM_001126116.1&NM_001276698.2,c.67_70dup,HIGH,,,,-1;TP53,frameshift_variant,p.R24Hfs*26,ENST00000504290,,c.67_70dup,HIGH,,,,-1;TP53,frameshift_variant,p.R24Hfs*26,ENST00000504937,,c.67_70dup,HIGH,,,,-1;TP53,frameshift_variant,p.R156Hfs*26,ENST00000359597,,c.463_466dup,HIGH,,,,-1;TP53,frameshift_variant,p.R156Hfs*26,ENST00000413465,,c.463_466dup,HIGH,,,,-1;TP53,frameshift_variant,p.R24Hfs*26,ENST00000509690,,c.67_70dup,HIGH,,,,-1;TP53,frameshift_variant,p.R156Hfs*?,ENST00000508793,,c.463_466dup,HIGH,,,,-1;TP53,frameshift_variant,p.R63Hfs*26,ENST00000514944,,c.184_187dup,HIGH,,,,-1;TP53,5_prime_UTR_variant,,ENST00000618944,,c.-15_-12dup,MODIFIER,,,,-1;TP53,5_prime_UTR_variant,,ENST00000610623,NM_001126117.1&NM_001276699.2,c.-15_-12dup,MODIFIER,,,,-1;TP53,5_prime_UTR_variant,,ENST00000619186,NM_001126115.1&NM_001276697.2,c.-15_-12dup,MODIFIER,,,,-1;TP53,downstream_gene_variant,,ENST00000503591,,,MODIFIER,,,,-1;TP53,upstream_gene_variant,,ENST00000576024,,,MODIFIER,,,,-1;TP53,downstream_gene_variant,,ENST00000604348,,,MODIFIER,,,,-1;TP53,upstream_gene_variant,,ENST00000574684,,,MODIFIER,,,,-1;TP53,frameshift_variant,p.R117Hfs*26,ENST00000635293,,c.346_349dup,HIGH,,,,-1;TP53,non_coding_transcript_exon_variant,,ENST00000505014,,n.719_722dup,MODIFIER,,,,-1\tGGGT\tENSG00000141510\tENST00000269305\tTranscript\tframeshift_variant\tframeshift_variant\t608-609/2512\t466-467/1182\t156/393\tR/HPX\tcgc/cACCCgc\tCOSV52974259;COSV53384084\t\t-1\tTP53\tHGNC\tHGNC:11998\tprotein_coding\tYES\tCCDS11118.1\tENSP00000269305\tP04637.285\tK7PPA8.70\tUPI000002ED67\tP04637-1\tNM_000546.6\tNM_000546.6\tP1\t\t\t\t5/11\t\tPDB-ENSP_mappings:1gzh.A;PDB-ENSP_mappings:1gzh.C;PDB-ENSP_mappings:1kzy.A;PDB-ENSP_mappings:1kzy.B;PDB-ENSP_mappings:1tsr.A;PDB-ENSP_mappings:1tsr.B;PDB-ENSP_mappings:1tsr.C;PDB-ENSP_mappings:1tup.A;PDB-ENSP_mappings:1tup.B;PDB-ENSP_mappings:1tup.C;PDB-ENSP_mappings:1uol.A;PDB-ENSP_mappings:1uol.B;PDB-ENSP_mappings:1ycs.A;Gene3D:2.60.40.720;PDB-ENSP_mappings:2ac0.A;PDB-ENSP_mappings:2ac0.B;PDB-ENSP_mappings:2ac0.C;PDB-ENSP_mappings:2ac0.D;PDB-ENSP_mappings:2ady.A;PDB-ENSP_mappings:2ady.B;PDB-ENSP_mappings:2ahi.A;PDB-ENSP_mappings:2ahi.B;PDB-ENSP_mappings:2ahi.C;PDB-ENSP_mappings:2ahi.D;PDB-ENSP_mappings:2ata.A;PDB-ENSP_mappings:2ata.B;PDB-ENSP_mappings:2ata.C;PDB-ENSP_mappings:2ata.D;PDB-ENSP_mappings:2bim.A;PDB-ENSP_mappings:2bim.B;PDB-ENSP_mappings:2bin.A;PDB-ENSP_mappings:2bio.A;PDB-ENSP_mappings:2bip.A;PDB-ENSP_mappings:2biq.A;PDB-ENSP_mappings:2fej.A;PDB-ENSP_mappings:2h1l.M;PDB-ENSP_mappings:2h1l.N;PDB-ENSP_mappings:2h1l.O;PDB-ENSP_mappings:2h1l.P;PDB-ENSP_mappings:2h1l.Q;PDB-ENSP_mappings:2h1l.R;PDB-ENSP_mappings:2h1l.S;PDB-ENSP_mappings:2h1l.T;PDB-ENSP_mappings:2h1l.U;PDB-ENSP_mappings:2h1l.V;PDB-ENSP_mappings:2h1l.W;PDB-ENSP_mappings:2h1l.X;PDB-ENSP_mappings:2j1w.A;PDB-ENSP_mappings:2j1w.B;PDB-ENSP_mappings:2j1x.A;PDB-ENSP_mappings:2j1x.B;PDB-ENSP_mappings:2j1y.A;PDB-ENSP_mappings:2j1y.B;PDB-ENSP_mappings:2j1y.C;PDB-ENSP_mappings:2j1y.D;PDB-ENSP_mappings:2j1z.A;PDB-ENSP_mappings:2j1z.B;PDB-ENSP_mappings:2j20.A;PDB-ENSP_mappings:2j20.B;PDB-ENSP_mappings:2j21.A;PDB-ENSP_mappings:2j21.B;PDB-ENSP_mappings:2mej.B;PDB-ENSP_mappings:2ocj.A;PDB-ENSP_mappings:2ocj.B;PDB-ENSP_mappings:2ocj.C;PDB-ENSP_mappings:2ocj.D;PDB-ENSP_mappings:2pcx.A;PDB-ENSP_mappings:2vuk.A;PDB-ENSP_mappings:2vuk.B;PDB-ENSP_mappings:2wgx.A;PDB-ENSP_mappings:2wgx.B;PDB-ENSP_mappings:2x0u.A;PDB-ENSP_mappings:2x0u.B;PDB-ENSP_mappings:2x0v.A;PDB-ENSP_mappings:2x0v.B;PDB-ENSP_mappings:2x0w.A;PDB-ENSP_mappings:2x0w.B;PDB-ENSP_mappings:2xwr.A;PDB-ENSP_mappings:2xwr.B;PDB-ENSP_mappings:2ybg.A;PDB-ENSP_mappings:2ybg.B;PDB-ENSP_mappings:2ybg.C;PDB-ENSP_mappings:2ybg.D;PDB-ENSP_mappings:3d05.A;PDB-ENSP_mappings:3d06.A;PDB-ENSP_mappings:3d07.A;PDB-ENSP_mappings:3d07.B;PDB-ENSP_mappings:3d08.A;PDB-ENSP_mappings:3d09.A;PDB-ENSP_mappings:3d0a.A;PDB-ENSP_mappings:3d0a.B;PDB-ENSP_mappings:3d0a.C;PDB-ENSP_mappings:3d0a.D;PDB-ENSP_mappings:3igk.A;PDB-ENSP_mappings:3igl.A;PDB-ENSP_mappings:3kmd.A;PDB-ENSP_mappings:3kmd.B;PDB-ENSP_mappings:3kmd.C;PDB-ENSP_mappings:3kmd.D;PDB-ENSP_mappings:3kz8.A;PDB-ENSP_mappings:3kz8.B;PDB-ENSP_mappings:3q01.A;PDB-ENSP_mappings:3q01.B;PDB-ENSP_mappings:3q05.A;PDB-ENSP_mappings:3q05.B;PDB-ENSP_mappings:3q05.C;PDB-ENSP_mappings:3q05.D;PDB-ENSP_mappings:3q06.A;PDB-ENSP_mappings:3q06.B;PDB-ENSP_mappings:3q06.C;PDB-ENSP_mappings:3q06.D;PDB-ENSP_mappings:3ts8.A;PDB-ENSP_mappings:3ts8.B;PDB-ENSP_mappings:3ts8.C;PDB-ENSP_mappings:3ts8.D;PDB-ENSP_mappings:3zme.A;PDB-ENSP_mappings:3zme.B;PDB-ENSP_mappings:4agl.A;PDB-ENSP_mappings:4agl.B;PDB-ENSP_mappings:4agm.A;PDB-ENSP_mappings:4agm.B;PDB-ENSP_mappings:4agn.A;PDB-ENSP_mappings:4agn.B;PDB-ENSP_mappings:4ago.A;PDB-ENSP_mappings:4ago.B;PDB-ENSP_mappings:4agp.A;PDB-ENSP_mappings:4agp.B;PDB-ENSP_mappings:4agq.A;PDB-ENSP_mappings:4agq.B;PDB-ENSP_mappings:4hje.A;PDB-ENSP_mappings:4hje.B;PDB-ENSP_mappings:4hje.C;PDB-ENSP_mappings:4hje.D;PDB-ENSP_mappings:4ibq.A;PDB-ENSP_mappings:4ibq.B;PDB-ENSP_mappings:4ibq.C;PDB-ENSP_mappings:4ibq.D;PDB-ENSP_mappings:4ibs.A;PDB-ENSP_mappings:4ibs.B;PDB-ENSP_mappings:4ibs.C;PDB-ENSP_mappings:4ibs.D;PDB-ENSP_mappings:4ibt.A;PDB-ENSP_mappings:4ibt.B;PDB-ENSP_mappings:4ibt.C;PDB-ENSP_mappings:4ibt.D;PDB-ENSP_mappings:4ibu.A;PDB-ENSP_mappings:4ibu.B;PDB-ENSP_mappings:4ibu.C;PDB-ENSP_mappings:4ibu.D;PDB-ENSP_mappings:4ibv.A;PDB-ENSP_mappings:4ibw.A;PDB-ENSP_mappings:4iby.A;PDB-ENSP_mappings:4iby.B;PDB-ENSP_mappings:4ibz.A;PDB-ENSP_mappings:4ibz.B;PDB-ENSP_mappings:4ibz.C;PDB-ENSP_mappings:4ibz.D;PDB-ENSP_mappings:4ijt.A;PDB-ENSP_mappings:4kvp.A;PDB-ENSP_mappings:4kvp.B;PDB-ENSP_mappings:4kvp.C;PDB-ENSP_mappings:4kvp.D;PDB-ENSP_mappings:4lo9.A;PDB-ENSP_mappings:4lo9.B;PDB-ENSP_mappings:4lo9.C;PDB-ENSP_mappings:4lo9.D;PDB-ENSP_mappings:4loe.A;PDB-ENSP_mappings:4loe.B;PDB-ENSP_mappings:4loe.C;PDB-ENSP_mappings:4loe.D;PDB-ENSP_mappings:4lof.A;PDB-ENSP_mappings:4mzi.A;PDB-ENSP_mappings:4mzr.A;PDB-ENSP_mappings:4mzr.B;PDB-ENSP_mappings:4mzr.C;PDB-ENSP_mappings:4mzr.D;PDB-ENSP_mappings:4qo1.B;PDB-ENSP_mappings:4xr8.C;PDB-ENSP_mappings:4xr8.D;PDB-ENSP_mappings:5a7b.A;PDB-ENSP_mappings:5a7b.B;PDB-ENSP_mappings:5ab9.A;PDB-ENSP_mappings:5ab9.B;PDB-ENSP_mappings:5aba.A;PDB-ENSP_mappings:5aba.B;PDB-ENSP_mappings:5aoi.A;PDB-ENSP_mappings:5aoi.B;PDB-ENSP_mappings:5aoj.A;PDB-ENSP_mappings:5aoj.B;PDB-ENSP_mappings:5aok.A;PDB-ENSP_mappings:5aok.B;PDB-ENSP_mappings:5aol.A;PDB-ENSP_mappings:5aol.B;PDB-ENSP_mappings:5aom.A;PDB-ENSP_mappings:5aom.B;PDB-ENSP_mappings:5bua.A;PDB-ENSP_mappings:5ecg.A;PDB-ENSP_mappings:5ecg.B;PDB-ENSP_mappings:5g4m.A;PDB-ENSP_mappings:5g4m.B;PDB-ENSP_mappings:5g4n.A;PDB-ENSP_mappings:5g4n.B;PDB-ENSP_mappings:5g4o.A;PDB-ENSP_mappings:5g4o.B;PDB-ENSP_mappings:5lap.A;PDB-ENSP_mappings:5lap.B;PDB-ENSP_mappings:5lgy.A;PDB-ENSP_mappings:5lgy.B;PDB-ENSP_mappings:5lgy.C;PDB-ENSP_mappings:5lgy.D;PDB-ENSP_mappings:5mct.A;PDB-ENSP_mappings:5mct.B;PDB-ENSP_mappings:5mcu.A;PDB-ENSP_mappings:5mcu.B;PDB-ENSP_mappings:5mcv.A;PDB-ENSP_mappings:5mcv.B;PDB-ENSP_mappings:5mcw.A;PDB-ENSP_mappings:5mcw.B;PDB-ENSP_mappings:5mf7.A;PDB-ENSP_mappings:5mf7.B;PDB-ENSP_mappings:5mg7.A;PDB-ENSP_mappings:5mg7.B;PDB-ENSP_mappings:5o1a.A;PDB-ENSP_mappings:5o1a.B;PDB-ENSP_mappings:5o1b.A;PDB-ENSP_mappings:5o1b.B;PDB-ENSP_mappings:5o1c.A;PDB-ENSP_mappings:5o1c.B;PDB-ENSP_mappings:5o1d.A;PDB-ENSP_mappings:5o1d.B;PDB-ENSP_mappings:5o1e.A;PDB-ENSP_mappings:5o1e.B;PDB-ENSP_mappings:5o1f.A;PDB-ENSP_mappings:5o1f.B;PDB-ENSP_mappings:5o1g.A;PDB-ENSP_mappings:5o1g.B;PDB-ENSP_mappings:5o1h.A;PDB-ENSP_mappings:5o1h.B;PDB-ENSP_mappings:5o1i.A;PDB-ENSP_mappings:5o1i.B;PDB-ENSP_mappings:5xzc.B;PDB-ENSP_mappings:5xzc.C;PDB-ENSP_mappings:5xzc.D;PDB-ENSP_mappings:5xzc.E;PDB-ENSP_mappings:6ff9.A;PDB-ENSP_mappings:6ff9.B;PDB-ENSP_mappings:6ff9.C;PDB-ENSP_mappings:6ff9.D;PDB-ENSP_mappings:6fj5.A;PDB-ENSP_mappings:6fj5.B;PDB-ENSP_mappings:6fj5.C;PDB-ENSP_mappings:6fj5.D;PDB-ENSP_mappings:6gga.A;PDB-ENSP_mappings:6gga.B;PDB-ENSP_mappings:6ggb.A;PDB-ENSP_mappings:6ggb.B;PDB-ENSP_mappings:6ggc.A;PDB-ENSP_mappings:6ggc.B;PDB-ENSP_mappings:6ggd.A;PDB-ENSP_mappings:6ggd.B;PDB-ENSP_mappings:6gge.A;PDB-ENSP_mappings:6gge.B;PDB-ENSP_mappings:6ggf.A;PDB-ENSP_mappings:6ggf.B;PDB-ENSP_mappings:6rz3.A;PDB-ENSP_mappings:6shz.A;PDB-ENSP_mappings:6shz.B;PDB-ENSP_mappings:6si0.A;PDB-ENSP_mappings:6si0.B;PDB-ENSP_mappings:6si1.A;PDB-ENSP_mappings:6si1.B;PDB-ENSP_mappings:6si2.A;PDB-ENSP_mappings:6si2.B;PDB-ENSP_mappings:6si3.A;PDB-ENSP_mappings:6si3.B;PDB-ENSP_mappings:6si4.A;PDB-ENSP_mappings:6si4.B;PDB-ENSP_mappings:6sl6.A;Pfam:PF00870;PANTHER:PTHR11447;PANTHER:PTHR11447:SF6;Superfamily:SSF49417;CDD:cd08367\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tHIGH\t1\tinsertion\t1\t\t1;1\t1\tGGACGCGGGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmutect2;pindel;varscan2\nCHD3\t1107\tBI\tGRCh38\tchr17\t7906583\t7906583\t+\tSilent\tSNP\tG\tG\tT\trs568783199\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.4389G>T\tp.Leu1463=\tp.L1463=\tENST00000330494\t29/40\t168\t122\t46\t156\t\t\tCHD3,synonymous_variant,p.L1463=,ENST00000330494,NM_001005273.3,c.4389G>T,LOW,,,,1;CHD3,synonymous_variant,p.L1522=,ENST00000380358,NM_001005271.3,c.4566G>T,LOW,YES,,,1;CHD3,synonymous_variant,p.L1463=,ENST00000358181,NM_005852.4,c.4389G>T,LOW,,,,1;CHD3,upstream_gene_variant,,ENST00000439235,,,MODIFIER,,,,1;CHD3,upstream_gene_variant,,ENST00000449744,,,MODIFIER,,,,1;CHD3,upstream_gene_variant,,ENST00000573936,,,MODIFIER,,,,1;CHD3,downstream_gene_variant,,ENST00000672838,,,MODIFIER,,,,1;SCARNA21,downstream_gene_variant,,ENST00000517026,,,MODIFIER,YES,,,1;CHD3,3_prime_UTR_variant,,ENST00000470531,,c.*760G>T,MODIFIER,,,,1;CHD3,downstream_gene_variant,,ENST00000466233,,,MODIFIER,,,,1;CHD3,downstream_gene_variant,,ENST00000473376,,,MODIFIER,,,,1;CHD3,upstream_gene_variant,,ENST00000481999,,,MODIFIER,,,,1;CHD3,upstream_gene_variant,,ENST00000572750,,,MODIFIER,,,,1\tT\tENSG00000170004\tENST00000330494\tTranscript\tsynonymous_variant\tsynonymous_variant\t4601/7385\t4389/6003\t1463/2000\tL\tctG/ctT\trs568783199;COSV100391683\t\t1\tCHD3\tHGNC\tHGNC:1918\tprotein_coding\t\tCCDS32554.1\tENSP00000332628\tQ12873.212\t\tUPI00001AED64\tQ12873-1\tNM_001005273.3\tNM_001005273.3\tP4\t\t\t\t29/40\t\tPfam:PF06461;PANTHER:PTHR45623;PANTHER:PTHR45623:SF9;SMART:SM01146\t0.0002\t0.0\t0.0\t0.0\t0.001\t0.0\t\t\t3.978e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.793e-06\t0.0\t0.0\t0.001\tEUR\t6.766630122001516e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.5438799891853705e-05\t0.0\t0.0\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t0;1\t1\tCATCTGTGTGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nMYH13\t8735\tBI\tGRCh38\tchr17\t10301679\t10301679\t+\tMissense_Mutation\tSNP\tA\tA\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.5692T>C\tp.Ser1898Pro\tp.S1898P\tENST00000252172\t40/41\t59\t43\t16\t68\t\t\tMYH13,missense_variant,p.S1898P,ENST00000418404,,c.5692T>C,MODERATE,YES,deleterious(0),possibly_damaging(0.857),-1;MYH13,missense_variant,p.S1898P,ENST00000252172,NM_003802.3,c.5692T>C,MODERATE,,deleterious(0),possibly_damaging(0.857),-1;MYH13,missense_variant,p.S1898P,ENST00000621918,,c.5692T>C,MODERATE,,deleterious(0),possibly_damaging(0.857),-1;AC005291.2,intron_variant,,ENST00000609088,,n.94+9766A>G,MODIFIER,YES,,,1\tG\tENSG00000006788\tENST00000252172\tTranscript\tmissense_variant\tmissense_variant\t5783/5994\t5692/5817\t1898/1938\tS/P\tTcc/Ccc\tCOSV99355426\t\t-1\tMYH13\tHGNC\tHGNC:7571\tprotein_coding\t\tCCDS45613.1\tENSP00000252172\tQ9UKX3.177\t\tUPI0000DB39EA\t\tNM_003802.3\tNM_003802.3\tP1\t\tdeleterious(0)\tpossibly_damaging(0.857)\t40/41\t\tCoiled-coils_(Ncoils):Coil;Pfam:PF01576;PANTHER:PTHR45615;PANTHER:PTHR45615:SF5;Superfamily:SSF57997\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tTCTGGACAGCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNCOR1\t9611\tBI\tGRCh38\tchr17\t16108843\t16108843\t+\tNonsense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2125C>T\tp.Gln709Ter\tp.Q709*\tENST00000268712\t19/46\t101\t67\t34\t105\t\t\tNCOR1,stop_gained,p.Q709*,ENST00000268712,NM_006311.4,c.2125C>T,HIGH,YES,,,-1;NCOR1,stop_gained,p.Q600*,ENST00000395857,,c.1798C>T,HIGH,,,,-1;NCOR1,stop_gained,p.Q709*,ENST00000395851,NM_001190440.1,c.2125C>T,HIGH,,,,-1;NCOR1,stop_gained,p.Q600*,ENST00000395848,NM_001190438.1,c.1798C>T,HIGH,,,,-1;NCOR1,non_coding_transcript_exon_variant,,ENST00000583226,,n.517C>T,MODIFIER,,,,-1\tA\tENSG00000141027\tENST00000268712\tTranscript\tstop_gained\tstop_gained\t2368/10705\t2125/7323\t709/2440\tQ/*\tCag/Tag\tCOSV51960861\t\t-1\tNCOR1\tHGNC\tHGNC:7672\tprotein_coding\tYES\tCCDS11175.1\tENSP00000268712\tO75376.213\tA0A024RD47.52\tUPI000013D7D5\tO75376-1\tNM_006311.4\tNM_006311.4\tP3\t\t\t\t19/46\t\tPANTHER:PTHR13992;PANTHER:PTHR13992:SF5;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tHIGH\t1\tSNV\t1\t\t1\t1\tCTCCTGAGCAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM126825;COSM4767656\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSREBF1\t6720\tBI\tGRCh38\tchr17\t17819405\t17819405\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.761C>T\tp.Ala254Val\tp.A254V\tENST00000261646\t4/19\t121\t82\t39\t117\t\t\tSREBF1,missense_variant,p.A254V,ENST00000261646,NM_004176.4,c.761C>T,MODERATE,,deleterious(0),benign(0.176),-1;SREBF1,missense_variant,p.A284V,ENST00000355815,NM_001005291.3&NM_001321096.3,c.851C>T,MODERATE,YES,deleterious(0),benign(0.133),-1;SREBF1,missense_variant,p.A254V,ENST00000395757,,c.761C>T,MODERATE,,deleterious(0),benign(0.204),-1;SREBF1,missense_variant,p.A228V,ENST00000423161,,c.683C>T,MODERATE,,deleterious(0.01),benign(0.226),-1;SREBF1,non_coding_transcript_exon_variant,,ENST00000583732,,n.332C>T,MODIFIER,,,,-1;SREBF1,3_prime_UTR_variant,,ENST00000577897,,c.*118C>T,MODIFIER,,,,-1;SREBF1,non_coding_transcript_exon_variant,,ENST00000395751,,n.1377C>T,MODIFIER,,,,-1;SREBF1,non_coding_transcript_exon_variant,,ENST00000662439,,n.464C>T,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000395756,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000447641,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000469356,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000470247,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000471445,,,MODIFIER,,,,-1;SREBF1,downstream_gene_variant,,ENST00000476994,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000487401,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000490796,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000580540,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000581707,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000583080,,,MODIFIER,,,,-1;SREBF1,upstream_gene_variant,,ENST00000584760,,,MODIFIER,,,,-1\tA\tENSG00000072310\tENST00000261646\tTranscript\tmissense_variant\tmissense_variant\t955/4904\t761/3444\t254/1147\tA/V\tgCc/gTc\tCOSV99889462\t\t-1\tSREBF1\tHGNC\tHGNC:11289\tprotein_coding\t\tCCDS11189.1\tENSP00000261646\tP36956.211\t\tUPI0000141126\tP36956-1\tNM_004176.4\t\tP4\t\tdeleterious(0)\tbenign(0.176)\t4/19\t\tPANTHER:PTHR46062;PANTHER:PTHR46062:SF2\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tTCATGGCTGTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nKRT19\t3880\tBI\tGRCh38\tchr17\t41527918\t41527918\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.330G>A\tp.Val110=\tp.V110=\tENST00000361566\t1/6\t164\t124\t39\t134\t\t\tKRT19,splice_region_variant,,ENST00000455635,,c.327+3G>A,LOW,,,,-1;KRT19,synonymous_variant,p.V110=,ENST00000361566,NM_002276.5,c.330G>A,LOW,YES,,,-1;KRT19,upstream_gene_variant,,ENST00000593096,,,MODIFIER,,,,-1;KRT19,upstream_gene_variant,,ENST00000462611,,,MODIFIER,,,,-1;KRT19,upstream_gene_variant,,ENST00000468880,,,MODIFIER,,,,-1;KRT19,upstream_gene_variant,,ENST00000471565,,,MODIFIER,,,,-1;KRT19,upstream_gene_variant,,ENST00000479031,,,MODIFIER,,,,-1\tT\tENSG00000171345\tENST00000361566\tTranscript\tsynonymous_variant\tsynonymous_variant\t391/1390\t330/1203\t110/400\tV\tgtG/gtA\tCOSV100843700\t\t-1\tKRT19\tHGNC\tHGNC:6436\tprotein_coding\tYES\tCCDS11399.1\tENSP00000355124\tP08727.206\t\tUPI000006D379\t\tNM_002276.5\tNM_002276.5\tP1\t\t\t\t1/6\t\tCoiled-coils_(Ncoils):Coil;Pfam:PF00038;PROSITE_profiles:PS51842;PANTHER:PTHR23239;PANTHER:PTHR23239:SF14;SMART:SM01391;Superfamily:SSF64593\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tATCTTCACCTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nATXN7L3\t56970\tBI\tGRCh38\tchr17\t44194364\t44194364\t+\tMissense_Mutation\tSNP\tG\tG\tC\trs1488374974\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.943C>G\tp.Leu315Val\tp.L315V\tENST00000389384\t12/12\t137\t107\t29\t94\t\t\tATXN7L3,missense_variant,p.L315V,ENST00000389384,NM_001382309.1&NM_001382316.1&NM_001382314.1&NM_001382311.1&NM_001382313.1&NM_001382312.1&NM_001382315.1,c.943C>G,MODERATE,,tolerated_low_confidence(0.18),benign(0.003),-1;ATXN7L3,missense_variant,p.L322V,ENST00000454077,NM_001382308.1&NM_001382310.1,c.964C>G,MODERATE,YES,tolerated_low_confidence(0.19),benign(0.007),-1;ATXN7L3,missense_variant,p.L154V,ENST00000591295,,c.460C>G,MODERATE,,tolerated_low_confidence(0.17),probably_damaging(0.99),-1;TMUB2,downstream_gene_variant,,ENST00000319511,NM_177441.4&NM_001353175.2,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000357984,NM_024107.3&NM_001353191.2&NM_001353176.2&NM_001353178.2&NM_001353188.2&NM_001353183.2,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000446571,NM_001330235.2&NM_001353185.2&NM_001353180.2&NM_001353189.2&NM_001353187.2&NM_001353174.2,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000538716,NM_001353177.2&NM_001076674.3&NM_001353181.2&NM_001353184.2,,MODIFIER,YES,,,1;ATXN7L3,downstream_gene_variant,,ENST00000587097,,,MODIFIER,,,,-1;TMUB2,downstream_gene_variant,,ENST00000587172,,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000587630,,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000587989,,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000589184,,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000589785,NM_001353190.2&NM_001353173.2&NM_001353182.2,,MODIFIER,,,,1;ATXN7L3,downstream_gene_variant,,ENST00000589805,,,MODIFIER,,,,-1;TMUB2,downstream_gene_variant,,ENST00000589856,,,MODIFIER,,,,1;ATXN7L3,downstream_gene_variant,,ENST00000590169,,,MODIFIER,,,,-1;TMUB2,downstream_gene_variant,,ENST00000590235,NM_001353186.2,,MODIFIER,,,,1;ATXN7L3,downstream_gene_variant,,ENST00000590537,,,MODIFIER,,,,-1;TMUB2,downstream_gene_variant,,ENST00000592825,,,MODIFIER,,,,1;ATXN7L3,non_coding_transcript_exon_variant,,ENST00000593073,,n.403C>G,MODIFIER,,,,-1;ATXN7L3,downstream_gene_variant,,ENST00000586688,,,MODIFIER,,,,-1;ATXN7L3,downstream_gene_variant,,ENST00000587022,,,MODIFIER,,,,-1;TMUB2,downstream_gene_variant,,ENST00000587326,,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000587775,,,MODIFIER,,,,1;TMUB2,downstream_gene_variant,,ENST00000588413,,,MODIFIER,,,,1;ATXN7L3,downstream_gene_variant,,ENST00000589607,,,MODIFIER,,,,-1;ATXN7L3,downstream_gene_variant,,ENST00000591807,,,MODIFIER,,,,-1;AC004596.1,upstream_gene_variant,,ENST00000586560,,,MODIFIER,YES,,,1\tC\tENSG00000087152\tENST00000389384\tTranscript\tmissense_variant\tmissense_variant\t1252/3811\t943/1044\t315/347\tL/V\tCtg/Gtg\trs1488374974;COSV100116332\t\t-1\tATXN7L3\tHGNC\tHGNC:25416\tprotein_coding\t\tCCDS42345.1\tENSP00000374035\tQ14CW9.116\t\tUPI0000DA6BB8\tQ14CW9-1\tNM_001382309.1;NM_001382316.1;NM_001382314.1;NM_001382311.1;NM_001382313.1;NM_001382312.1;NM_001382315.1\t\tA1\t\ttolerated_low_confidence(0.18)\tbenign(0.003)\t12/12\t\tPANTHER:PTHR46367;PANTHER:PTHR46367:SF2;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t0;1\t\tGCTCAGATGGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nUBTF\t7343\tBI\tGRCh38\tchr17\t44210857\t44210857\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1294C>T\tp.Leu432Phe\tp.L432F\tENST00000302904\t13/21\t14\t8\t6\t10\t\t\tUBTF,missense_variant,p.L432F,ENST00000302904,,c.1294C>T,MODERATE,YES,tolerated(0.05),possibly_damaging(0.697),-1;UBTF,missense_variant,p.L432F,ENST00000436088,NM_014233.4,c.1294C>T,MODERATE,,tolerated(0.05),possibly_damaging(0.697),-1;UBTF,missense_variant,p.L395F,ENST00000343638,NM_001076683.2,c.1183C>T,MODERATE,,deleterious(0.04),benign(0.387),-1;UBTF,missense_variant,p.L395F,ENST00000533177,,c.1183C>T,MODERATE,,deleterious(0.04),benign(0.387),-1;UBTF,missense_variant,p.L395F,ENST00000527034,,c.1183C>T,MODERATE,,deleterious(0.03),possibly_damaging(0.564),-1;UBTF,missense_variant,p.L395F,ENST00000393606,NM_001076684.3,c.1183C>T,MODERATE,,deleterious(0.04),benign(0.387),-1;UBTF,missense_variant,p.L432F,ENST00000529383,,c.1294C>T,MODERATE,,tolerated(0.05),possibly_damaging(0.697),-1;UBTF,missense_variant,p.L395F,ENST00000526094,,c.1183C>T,MODERATE,,deleterious(0.04),benign(0.387),-1;UBTF,missense_variant,p.L19F,ENST00000529373,,c.55C>T,MODERATE,,tolerated(0.11),possibly_damaging(0.697),-1;UBTF,downstream_gene_variant,,ENST00000530828,,,MODIFIER,,,,-1;MIR6782,upstream_gene_variant,,ENST00000619539,,,MODIFIER,YES,,,-1;UBTF,downstream_gene_variant,,ENST00000537550,,,MODIFIER,,,,-1;UBTF,downstream_gene_variant,,ENST00000529042,,,MODIFIER,,,,-1;UBTF,upstream_gene_variant,,ENST00000529947,,,MODIFIER,,,,-1;UBTF,upstream_gene_variant,,ENST00000531368,,,MODIFIER,,,,-1;AC004596.1,intron_variant,,ENST00000586560,,n.54-5234G>A,MODIFIER,YES,,,1\tA\tENSG00000108312\tENST00000302904\tTranscript\tmissense_variant\tmissense_variant\t1787/4997\t1294/2295\t432/764\tL/F\tCtc/Ttc\tCOSV100256135\t\t-1\tUBTF\tHGNC\tHGNC:12511\tprotein_coding\tYES\tCCDS11480.1\tENSP00000302640\tP17480.215\t\tUPI000013797C\tP17480-1\t\t\tP1\t\ttolerated(0.05)\tpossibly_damaging(0.697)\t13/21\t\tGene3D:1.10.30.10;Pfam:PF00505;PROSITE_profiles:PS50118;PANTHER:PTHR46318;PANTHER:PTHR46318:SF4;SMART:SM00398;Superfamily:SSF47095;CDD:cd01390\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t2\t\t1\t1\tGGAGAGCTCAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSEPTIN4\t5414\tBI\tGRCh38\tchr17\t58526699\t58526699\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.340C>G\tp.Pro114Ala\tp.P114A\tENST00000317268\t2/12\t118\t110\t8\t70\t\t\tSEPTIN4,missense_variant,p.P632A,ENST00000672673,NM_001368772.1&NM_001368771.2,c.1894C>G,MODERATE,YES,deleterious_low_confidence(0.01),probably_damaging(0.972),-1;SEPTIN4,missense_variant,p.P95A,ENST00000426861,NM_080415.3,c.283C>G,MODERATE,,deleterious_low_confidence(0.02),possibly_damaging(0.661),-1;SEPTIN4,missense_variant,p.P129A,ENST00000457347,,c.385C>G,MODERATE,,deleterious(0.02),probably_damaging(0.997),-1;SEPTIN4,missense_variant,p.P129A,ENST00000672699,NM_001256782.1,c.385C>G,MODERATE,,deleterious(0.02),probably_damaging(0.997),-1;SEPTIN4,missense_variant,p.P114A,ENST00000317268,NM_004574.4,c.340C>G,MODERATE,,deleterious(0),possibly_damaging(0.577),-1;SEPTIN4,missense_variant,p.P106A,ENST00000412945,NM_001198713.1,c.316C>G,MODERATE,,deleterious(0),possibly_damaging(0.523),-1;SEPTIN4,missense_variant,p.P95A,ENST00000393086,,c.283C>G,MODERATE,,deleterious(0.01),possibly_damaging(0.523),-1;SEPTIN4,missense_variant,p.P95A,ENST00000317256,NM_080416.3,c.283C>G,MODERATE,,deleterious(0.01),possibly_damaging(0.523),-1;SEPTIN4,missense_variant,p.P119A,ENST00000583291,,c.355C>G,MODERATE,,deleterious(0.01),probably_damaging(0.999),-1;SEPTIN4,missense_variant,p.P107A,ENST00000671766,,c.319C>G,MODERATE,,deleterious(0.01),probably_damaging(0.968),-1;SEPTIN4,5_prime_UTR_variant,,ENST00000583114,NM_001256822.1,c.-102C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000577729,,c.76-386C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000579371,,c.61-386C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000580809,,c.4-386C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000580844,NM_001363803.1,c.61-386C>G,MODIFIER,,,,-1;SEPTIN4,downstream_gene_variant,,ENST00000581607,,,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000580791,,n.453C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000584528,,n.385C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000580740,,n.427C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000581921,,n.48-289C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000585170,,n.1871C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000580796,,n.1155C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000583273,,n.516C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000577440,,n.370C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000584488,,n.479C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000584789,,n.357C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000582248,,n.468C>G,MODIFIER,,,,-1;SEPTIN4,non_coding_transcript_exon_variant,,ENST00000578747,,n.443C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000578131,,c.50+233C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000581615,,c.107+233C>G,MODIFIER,,,,-1;SEPTIN4,intron_variant,,ENST00000582270,,n.301+68C>G,MODIFIER,,,,-1;SEPTIN4,downstream_gene_variant,,ENST00000582976,,,MODIFIER,,,,-1;SEPTIN4-AS1,intron_variant,,ENST00000578022,,n.358+882G>C,MODIFIER,YES,,,1;SEPTIN4-AS1,intron_variant,,ENST00000580589,,n.258+882G>C,MODIFIER,,,,1;SEPTIN4-AS1,intron_variant,,ENST00000580769,,n.149+882G>C,MODIFIER,,,,1\tC\tENSG00000108387\tENST00000317268\tTranscript\tmissense_variant\tmissense_variant\t517/1784\t340/1437\t114/478\tP/A\tCcc/Gcc\tCOSV100422168\t\t-1\tSEPTIN4\tHGNC\tHGNC:9165\tprotein_coding\t\tCCDS11610.1\tENSP00000321674\tO43236.181\t\tUPI000013585C\tO43236-1\tNM_004574.4\t\t\t\tdeleterious(0)\tpossibly_damaging(0.577)\t2/12\t\tPANTHER:PTHR18884;PANTHER:PTHR18884:SF71\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tATAGGGATCAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nCLTC\t1213\tBI\tGRCh38\tchr17\t59685074\t59685074\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7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42G>C,MODERATE,,tolerated(0.13),possibly_damaging(0.773),-1;STRADA,missense_variant,p.E48Q,ENST00000638309,,c.142G>C,MODERATE,,tolerated(0.17),possibly_damaging(0.521),-1;STRADA,missense_variant,p.E48Q,ENST00000638193,,c.142G>C,MODERATE,,tolerated(0.12),benign(0.255),-1;STRADA,missense_variant,p.E48Q,ENST00000638698,,c.142G>C,MODERATE,,tolerated(0.17),possibly_damaging(0.892),-1;STRADA,missense_variant,p.E48Q,ENST00000578801,,c.142G>C,MODERATE,,tolerated(0.1),probably_damaging(0.962),-1;STRADA,missense_variant,p.E19Q,ENST00000582137,NM_001165969.2,c.55G>C,MODERATE,,tolerated(0.1),benign(0.061),-1;STRADA,missense_variant,p.E19Q,ENST00000578008,,c.55G>C,MODERATE,,tolerated(0.14),possibly_damaging(0.886),-1;STRADA,missense_variant,p.E40Q,ENST00000640174,,c.118G>C,MODERATE,,tolerated(0.06),possibly_damaging(0.773),-1;STRADA,missense_variant,p.E48Q,ENST00000640397,,c.142G>C,MODERATE,,tolerated_low_confidence(0.07),possibly_damaging(0.852),-1;STRADA,missense_variant,p.E48Q,ENST00000579549,,c.142G>C,MODERATE,,tolerated(0.16),benign(0.398),-1;STRADA,missense_variant,p.E11Q,ENST00000639135,,c.31G>C,MODERATE,,tolerated(0.09),possibly_damaging(0.825),-1;STRADA,missense_variant,p.E19Q,ENST00000639603,,c.55G>C,MODERATE,,deleterious(0.02),probably_damaging(0.936),-1;STRADA,5_prime_UTR_variant,,ENST00000245865,,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000375840,NM_001003788.3,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000638702,,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000640979,NM_001363790.1,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000638276,NM_001363791.1,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000579340,,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000638718,,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000582030,,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000580338,,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000584110,,c.-33G>C,MODIFIER,,,,-1;STRADA,5_prime_UTR_variant,,ENST00000580288,,c.-33G>C,MODIFIER,,,,-1;STRADA,intron_variant,,ENST00000447001,NM_001165970.2,c.95-563G>C,MODIFIER,,,,-1;STRADA,intron_variant,,ENST00000640741,,c.-104-563G>C,MODIFIER,,,,-1;STRADA,upstream_gene_variant,,ENST00000617949,,,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000639816,,n.186G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000639778,,n.131G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000579350,,n.366G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000640924,,n.356G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000639940,,n.238G>C,MODIFIER,,,,-1;STRADA,missense_variant,p.E13Q,ENST00000640870,,c.37G>C,MODERATE,,deleterious_low_confidence(0.01),possibly_damaging(0.898),-1;STRADA,missense_variant,p.E48Q,ENST00000640827,,c.142G>C,MODERATE,,tolerated(0.1),possibly_damaging(0.767),-1;STRADA,missense_variant,p.E11Q,ENST00000639521,,c.31G>C,MODERATE,,deleterious_low_confidence(0.05),probably_damaging(0.938),-1;STRADA,missense_variant,p.Q45H,ENST00000639164,,c.135G>C,MODERATE,,,unknown(0),-1;AC046185.1,3_prime_UTR_variant,,ENST00000580553,,c.*180G>C,MODIFIER,YES,,,-1;STRADA,3_prime_UTR_variant,,ENST00000581243,,c.*70G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000640183,,n.1735G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000579318,,n.465G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000640707,,n.693G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000639192,,n.314G>C,MODIFIER,,,,-1;STRADA,non_coding_transcript_exon_variant,,ENST00000577375,,n.128G>C,MODIFIER,,,,-1;STRADA,intron_variant,,ENST00000580039,,c.30-563G>C,MODIFIER,,,,-1;STRADA,intron_variant,,ENST00000581505,,c.30-563G>C,MODIFIER,,,,-1;STRADA,upstream_gene_variant,,ENST00000638578,,,MODIFIER,,,,-1\tG\tENSG00000266173\tENST00000336174\tTranscript\tmissense_variant\tmissense_variant\t245/2166\t142/1296\t48/431\tE/Q\tGag/Cag\tCOSV99835349\t\t-1\tSTRADA\tHGNC\tHGNC:30172\tprotein_coding\tYES\tCCDS32703.1\tENSP00000336655\tQ7RTN6.154\t\tUPI000013CBBE\tQ7RTN6-1\tNM_001363786.1;NM_001003787.4\tNM_001003787.4\tP1\t\ttolerated(0.19)\tbenign(0.398)\t5/13\t\tPANTHER:PTHR24361;PANTHER:PTHR24361:SF442\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t1\tTGACTCTGAGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSMURF2\t64750\tBI\tGRCh38\tchr17\t64562934\t64562934\t+\tMissense_Mutation\tSNP\tT\tT\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1049A>T\tp.Gln350Leu\tp.Q350L\tENST00000262435\t11/19\t51\t33\t18\t37\t\t\tSMURF2,missense_variant,p.Q350L,ENST00000262435,NM_022739.4,c.1049A>T,MODERATE,YES,tolerated(0.27),benign(0.001),-1;SMURF2,missense_variant,p.Q337L,ENST00000585301,,c.1010A>T,MODERATE,,tolerated(0.27),benign(0.001),-1;SMURF2,intron_variant,,ENST00000578200,,n.117-1331A>T,MODIFIER,,,,-1;SMURF2,3_prime_UTR_variant,,ENST00000582081,,c.*956A>T,MODIFIER,,,,-1;SMURF2,3_prime_UTR_variant,,ENST00000578386,,c.*871A>T,MODIFIER,,,,-1;SMURF2,non_coding_transcript_exon_variant,,ENST00000580072,,n.232A>T,MODIFIER,,,,-1\tA\tENSG00000108854\tENST00000262435\tTranscript\tmissense_variant\tmissense_variant\t1476/6240\t1049/2247\t350/748\tQ/L\tcAg/cTg\tCOSV99301061\t\t-1\tSMURF2\tHGNC\tHGNC:16809\tprotein_coding\tYES\tCCDS32707.1\tENSP00000262435\tQ9HAU4.195\t\tUPI00001361C5\t\tNM_022739.4\tNM_022739.4\tP1\t\ttolerated(0.27)\tbenign(0.001)\t11/19\t\tGene3D:3.90.1750.10;PANTHER:PTHR11254;PANTHER:PTHR11254:SF300;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCTTGCTGTTGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nGNA13\t10672\tBI\tGRCh38\tchr17\t65014699\t65014699\t+\tMissense_Mutation\tSNP\tT\tT\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.692A>T\tp.Lys231Ile\tp.K231I\tENST00000439174\t4/4\t122\t83\t39\t61\t\t\tGNA13,missense_variant,p.K231I,ENST00000439174,NM_006572.6,c.692A>T,MODERATE,YES,deleterious(0),possibly_damaging(0.541),-1;GNA13,missense_variant,p.K136I,ENST00000541118,NM_001282425.1,c.407A>T,MODERATE,,deleterious(0),possibly_damaging(0.541),-1\tA\tENSG00000120063\tENST00000439174\tTranscript\tmissense_variant\tmissense_variant\t839/6249\t692/1134\t231/377\tK/I\taAa/aTa\tCOSV101457514\t\t-1\tGNA13\tHGNC\tHGNC:4381\tprotein_coding\tYES\tCCDS11661.1\tENSP00000400717\tQ14344.189\tA0A024R8M0.44\tUPI0000073EBA\tQ14344-1\tNM_006572.6\tNM_006572.6\tP1\t\tdeleterious(0)\tpossibly_damaging(0.541)\t4/4\t\tGene3D:3.40.50.300;Pfam:PF00503;Prints:PR00318;PROSITE_profiles:PS51882;PANTHER:PTHR10218;PANTHER:PTHR10218:SF85;SMART:SM00275;Superfamily:SSF52540;CDD:cd00066\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tAACGTTTCCTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPITPNC1\t26207\tBI\tGRCh38\tchr17\t67675530\t67675530\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.670G>C\tp.Asp224His\tp.D224H\tENST00000581322\t8/9\t195\t158\t37\t99\t\t\tPITPNC1,missense_variant,p.D222H,ENST00000299954,,c.664G>C,MODERATE,,deleterious(0),probably_damaging(1),1;PITPNC1,missense_variant,p.D224H,ENST00000581322,NM_012417.4,c.670G>C,MODERATE,YES,deleterious(0),probably_damaging(1),1;PITPNC1,missense_variant,p.D224H,ENST00000580974,NM_181671.3,c.670G>C,MODERATE,,deleterious(0),probably_damaging(0.999),1;PITPNC1,non_coding_transcript_exon_variant,,ENST00000578527,,n.808G>C,MODIFIER,,,,1\tC\tENSG00000154217\tENST00000581322\tTranscript\tmissense_variant\tmissense_variant\t1544/6241\t670/999\t224/332\tD/H\tGat/Cat\tCOSV100084111;COSV55455070\t\t1\tPITPNC1\tHGNC\tHGNC:21045\tprotein_coding\tYES\tCCDS58588.1\tENSP00000464006\tQ9UKF7.123\t\tUPI00001AE46B\tQ9UKF7-1\tNM_012417.4\tNM_012417.4\tP3\t\tdeleterious(0)\tprobably_damaging(1)\t8/9\t\tGene3D:3.30.530.20;Pfam:PF02121;Prints:PR00391;PANTHER:PTHR10658;PANTHER:PTHR10658:SF55;Superfamily:SSF55961;CDD:cd08890\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1;1\t\tGGGTTGATGAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNOL11\t25926\tBI\tGRCh38\tchr17\t67721431\t67721431\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.366G>A\tp.Val122=\tp.V122=\tENST00000253247\t4/18\t187\t154\t33\t114\t\t\tNOL11,synonymous_variant,p.V122=,ENST00000253247,NM_001303272.1&NM_015462.5,c.366G>A,LOW,YES,,,1;NOL11,synonymous_variant,p.V141=,ENST00000581106,,c.423G>A,LOW,,,,1;NOL11,upstream_gene_variant,,ENST00000580833,,,MODIFIER,,,,1;NOL11,non_coding_transcript_exon_variant,,ENST00000581966,,n.467G>A,MODIFIER,,,,1;NOL11,synonymous_variant,p.V122=,ENST00000581375,,c.366G>A,LOW,,,,1;NOL11,non_coding_transcript_exon_variant,,ENST00000584942,,n.513G>A,MODIFIER,,,,1;NOL11,upstream_gene_variant,,ENST00000580914,,,MODIFIER,,,,1\tA\tENSG00000130935\tENST00000253247\tTranscript\tsynonymous_variant\tsynonymous_variant\t378/2844\t366/2160\t122/719\tV\tgtG/gtA\tCOSV99475295\t\t1\tNOL11\tHGNC\tHGNC:24557\tprotein_coding\tYES\tCCDS11671.1\tENSP00000253247\tQ9H8H0.145\t\tUPI0000072B83\tQ9H8H0-1\tNM_001303272.1;NM_015462.5\tNM_015462.5\tP1\t\t\t\t4/18\t\tPANTHER:PTHR15633;PANTHER:PTHR15633:SF3;Superfamily:SSF50978\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tTTGGTGCTCTT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nRECQL5\t9400\tBI\tGRCh38\tchr17\t75658431\t75658431\t+\tMissense_Mutation\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1016C>A\tp.Ser339Tyr\tp.S339Y\tENST00000317905\t7/20\t274\t174\t100\t183\t\t\tRECQL5,missense_variant,p.S339Y,ENST00000420326,NM_001003716.4,c.1016C>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;RECQL5,missense_variant,p.S339Y,ENST00000317905,NM_004259.7,c.1016C>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),-1;RECQL5,missense_variant,p.S312Y,ENST00000423245,,c.935C>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;RECQL5,missense_variant,p.S339Y,ENST00000578201,,c.1016C>A,MODERATE,,deleterious(0),probably_damaging(0.999),-1;RECQL5,missense_variant,p.S339Y,ENST00000584999,,c.1016C>A,MODERATE,,deleterious(0),probably_damaging(0.99),-1;RECQL5,missense_variant,p.S339Y,ENST00000340830,NM_001003715.4,c.1016C>A,MODERATE,,deleterious(0),probably_damaging(0.99),-1;RECQL5,synonymous_variant,p.V171=,ENST00000580078,,c.513C>A,LOW,,,,-1;RECQL5,upstream_gene_variant,,ENST00000579274,,,MODIFIER,,,,-1;RECQL5,missense_variant,p.S22Y,ENST00000582464,,c.65C>A,MODERATE,,deleterious(0),probably_damaging(0.996),-1\tT\tENSG00000108469\tENST00000317905\tTranscript\tmissense_variant\tmissense_variant\t1141/3669\t1016/2976\t339/991\tS/Y\ttCt/tAt\tCOSV100512348\t\t-1\tRECQL5\tHGNC\tHGNC:9950\tprotein_coding\tYES\tCCDS42380.1\tENSP00000317636\tO94762.199\tA0A024R8M9.54\tUPI0000133477\tO94762-1\tNM_004259.7\tNM_004259.7\tP1\t\tdeleterious(0)\tprobably_damaging(0.999)\t7/20\t\tGene3D:3.40.50.300;PDB-ENSP_mappings:5lb3.B;PDB-ENSP_mappings:5lb3.E;PDB-ENSP_mappings:5lb5.A;PDB-ENSP_mappings:5lb5.B;PDB-ENSP_mappings:5lb5.C;PDB-ENSP_mappings:5lb5.D;PDB-ENSP_mappings:5lb8.A;PDB-ENSP_mappings:5lb8.D;PDB-ENSP_mappings:5lba.A;PDB-ENSP_mappings:5lba.B;PDB-ENSP_mappings:5lba.C;PDB-ENSP_mappings:5lba.D;Pfam:PF00271;PROSITE_profiles:PS51194;PANTHER:PTHR13710;PANTHER:PTHR13710:SF124;SMART:SM00490;Superfamily:SSF52540;TIGRFAM:TIGR00614;CDD:cd18794\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCCATAGACTTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nGNAL\t2774\tBI\tGRCh38\tchr18\t11752441\t11752441\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.8G>A\tp.Cys3Tyr\tp.C3Y\tENST00000269162\t2/13\t196\t146\t50\t146\t\t\tGNAL,missense_variant,p.C3Y,ENST00000423027,NM_001369387.1,c.8G>A,MODERATE,,deleterious(0),possibly_damaging(0.804),1;GNAL,missense_variant,p.C3Y,ENST00000269162,NM_001142339.3,c.8G>A,MODERATE,,deleterious(0),possibly_damaging(0.804),1;GNAL,missense_variant,p.C3Y,ENST00000535121,NM_001261443.1,c.8G>A,MODERATE,,deleterious(0),possibly_damaging(0.804),1;GNAL,intron_variant,,ENST00000334049,NM_182978.4,c.377-412G>A,MODIFIER,YES,,,1;GNAL,upstream_gene_variant,,ENST00000585642,,,MODIFIER,,,,1;GNAL,upstream_gene_variant,,ENST00000590228,,,MODIFIER,,,,1;GNAL,upstream_gene_variant,,ENST00000590972,,,MODIFIER,,,,1;ASNSP6,downstream_gene_variant,,ENST00000592770,,,MODIFIER,YES,,,1\tA\tENSG00000141404\tENST00000269162\tTranscript\tmissense_variant\tmissense_variant\t309/1722\t8/1146\t3/381\tC/Y\ttGt/tAt\tCOSV99304183\t\t1\tGNAL\tHGNC\tHGNC:4388\tprotein_coding\t\tCCDS11852.1\tENSP00000269162\tP38405.186\tA8K1Y9.113\tUPI0000001246\tP38405-1\tNM_001142339.3\t\tP1\t\tdeleterious(0)\tpossibly_damaging(0.804)\t2/13\t\tMobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t2\t\t1\t1\tGGGGTGTTTGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNOL4\t8715\tBI\tGRCh38\tchr18\t33958266\t33958266\t+\tSilent\tSNP\tA\tA\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1209T>A\tp.Val403=\tp.V403=\tENST00000261592\t7/11\t77\t64\t12\t140\t\t\tNOL4,synonymous_variant,p.V403=,ENST00000261592,NM_001353232.1&NM_003787.4,c.1209T>A,LOW,YES,,,-1;NOL4,synonymous_variant,p.V403=,ENST00000589544,NM_001198548.1,c.1209T>A,LOW,,,,-1;NOL4,synonymous_variant,p.V329=,ENST00000538587,NM_001353234.1&NM_001198547.1&NM_001353235.1,c.987T>A,LOW,,,,-1;NOL4,synonymous_variant,p.V387=,ENST00000590712,NM_001198546.1&NM_001353237.1&NM_001282527.1,c.1161T>A,LOW,,,,-1;NOL4,synonymous_variant,p.V118=,ENST00000535384,NM_001353233.1&NM_001353236.1&NM_001198549.1,c.354T>A,LOW,,,,-1;NOL4,synonymous_variant,p.V152=,ENST00000586553,,c.456T>A,LOW,,,,-1;NOL4,3_prime_UTR_variant,,ENST00000586314,,c.*818T>A,MODIFIER,,,,-1\tT\tENSG00000101746\tENST00000261592\tTranscript\tsynonymous_variant\tsynonymous_variant\t1507/3957\t1209/1917\t403/638\tV\tgtT/gtA\tCOSV99308338\t\t-1\tNOL4\tHGNC\tHGNC:7870\tprotein_coding\tYES\tCCDS11907.2\tENSP00000261592\tO94818.142\t\tUPI000059D504\tO94818-1\tNM_001353232.1;NM_003787.4\t\tP1\t\t\t\t7/11\t\tPANTHER:PTHR12449;PANTHER:PTHR12449:SF17;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tGCTTCAACGCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nDTNA\t1837\tBI\tGRCh38\tchr18\t34858313\t34858313\t+\tMissense_Mutation\tSNP\tC\tC\tT\trs764410940\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1480C>T\tp.Arg494Trp\tp.R494W\tENST00000399113\t15/21\t38\t26\t12\t39\t\t\tDTNA,missense_variant,p.R437W,ENST00000283365,NM_032975.3,c.1309C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;DTNA,missense_variant,p.R434W,ENST00000399121,NM_001198939.2,c.1300C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;DTNA,missense_variant,p.R494W,ENST00000444659,NM_001390.4,c.1480C>T,MODERATE,YES,deleterious(0),probably_damaging(0.998),1;DTNA,missense_variant,p.R434W,ENST00000595022,NM_001198940.2,c.1300C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;DTNA,missense_variant,p.R491W,ENST00000348997,NM_032978.7&NM_001391.5,c.1471C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;DTNA,missense_variant,p.R434W,ENST00000598334,NM_001198938.2,c.1300C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;DTNA,missense_variant,p.R437W,ENST00000598142,,c.1309C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;DTNA,missense_variant,p.R437W,ENST00000598774,NM_032979.5,c.1309C>T,MODERATE,,deleterious(0),probably_damaging(0.994),1;DTNA,missense_variant,p.R494W,ENST00000399113,,c.1480C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;DTNA,missense_variant,p.R203W,ENST00000269192,NM_001198942.1,c.607C>T,MODERATE,,deleterious(0),probably_damaging(1),1;DTNA,missense_variant,p.R116W,ENST00000601125,NM_001198943.1,c.346C>T,MODERATE,,deleterious(0),probably_damaging(0.991),1;DTNA,missense_variant,p.R434W,ENST00000597599,NM_001198941.2,c.1300C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;DTNA,missense_variant,p.R142W,ENST00000591182,NM_032980.4,c.424C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;DTNA,missense_variant,p.R116W,ENST00000597674,NM_032981.5,c.346C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;DTNA,missense_variant,p.R146W,ENST00000556414,NM_001198944.1,c.436C>T,MODERATE,,deleterious(0),probably_damaging(0.998),1;DTNA,missense_variant,p.R244W,ENST00000596745,NM_001198945.2,c.730C>T,MODERATE,,deleterious(0),probably_damaging(0.999),1;DTNA,missense_variant,p.R116W,ENST00000599844,,c.346C>T,MODERATE,,deleterious(0),probably_damaging(0.975),1;DTNA,missense_variant,p.R93W,ENST00000587723,,c.277C>T,MODERATE,,deleterious(0),probably_damaging(0.997),1;DTNA,non_coding_transcript_exon_variant,,ENST00000601632,,n.754C>T,MODIFIER,,,,1;DTNA,non_coding_transcript_exon_variant,,ENST00000601895,,n.583C>T,MODIFIER,,,,1\tT\tENSG00000134769\tENST00000399113\tTranscript\tmissense_variant\tmissense_variant\t1480/2232\t1480/2232\t494/743\tR/W\tCgg/Tgg\trs764410940;COSV51993542\t\t1\tDTNA\tHGNC\tHGNC:3057\tprotein_coding\t\t\tENSP00000382064\tQ9Y4J8.191\t\tUPI000013DD3C\tQ9Y4J8-1\t\t\tA1\t\tdeleterious(0)\tprobably_damaging(0.998)\t15/21\t\tCoiled-coils_(Ncoils):Coil;CDD:cd16855;PANTHER:PTHR12268:SF19;PANTHER:PTHR12268;PIRSF:PIRSF038204\t\t\t\t\t\t\t\t\t7.987e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t1.774e-05\t0.0\t0.0\t1.774e-05\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t5\t\t0;1\t1\tGACTTCGGCTA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM1680331;COSM1680332;COSM185102;COSM185103;COSM4274846\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCXXC1\t30827\tBI\tGRCh38\tchr18\t50285815\t50285815\t+\tSilent\tSNP\tC\tC\tT\trs533080894\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.573G>A\tp.Lys191=\tp.K191=\tENST00000285106\t5/15\t118\t76\t42\t118\t\t\tCXXC1,synonymous_variant,p.K191=,ENST00000285106,NM_014593.3,c.573G>A,LOW,,,,-1;CXXC1,synonymous_variant,p.K191=,ENST00000673786,,c.573G>A,LOW,,,,-1;CXXC1,synonymous_variant,p.K191=,ENST00000589548,,c.573G>A,LOW,,,,-1;CXXC1,synonymous_variant,p.K191=,ENST00000412036,NM_001101654.1,c.573G>A,LOW,YES,,,-1;CXXC1,synonymous_variant,p.K191=,ENST00000589940,,c.573G>A,LOW,,,,-1;CXXC1,synonymous_variant,p.K39=,ENST00000591474,,c.117G>A,LOW,,,,-1;CXXC1,synonymous_variant,p.K191=,ENST00000586837,,c.573G>A,LOW,,,,-1;MBD1,upstream_gene_variant,,ENST00000269468,NM_001323950.1&NM_015846.3,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000269471,NM_001323953.1&NM_015845.3,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000339998,NM_001204142.2,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000347968,NM_001323952.1&NM_015844.2,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000353909,NM_015847.3,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000382948,NM_001204139.1,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000398493,,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000457839,NM_001323949.2&NM_001204138.2&NM_001204137.2,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000585595,,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000585672,NM_001204141.1&NM_001323951.1,,MODIFIER,,,,-1;CXXC1,downstream_gene_variant,,ENST00000587396,,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000587605,NM_001204143.2,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000590208,NM_001323954.1&NM_001204136.1&NM_001323947.1&NM_001323942.1,,MODIFIER,YES,,,-1;MBD1,upstream_gene_variant,,ENST00000591416,,,MODIFIER,,,,-1;CXXC1,non_coding_transcript_exon_variant,,ENST00000590901,,n.920G>A,MODIFIER,,,,-1;CXXC1,non_coding_transcript_exon_variant,,ENST00000591190,,n.423G>A,MODIFIER,,,,-1;CXXC1,non_coding_transcript_exon_variant,,ENST00000586365,,n.778G>A,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000586118,,,MODIFIER,,,,-1;CXXC1,upstream_gene_variant,,ENST00000586144,,,MODIFIER,,,,-1;CXXC1,upstream_gene_variant,,ENST00000586502,,,MODIFIER,,,,-1;CXXC1,upstream_gene_variant,,ENST00000586568,,,MODIFIER,,,,-1;CXXC1,upstream_gene_variant,,ENST00000587170,,,MODIFIER,,,,-1;CXXC1,upstream_gene_variant,,ENST00000587342,,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000589758,,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000589867,,,MODIFIER,,,,-1;MBD1,upstream_gene_variant,,ENST00000590215,,,MODIFIER,,,,-1;CXXC1,upstream_gene_variant,,ENST00000590234,,,MODIFIER,,,,-1;CXXC1,upstream_gene_variant,,ENST00000592078,,,MODIFIER,,,,-1\tT\tENSG00000154832\tENST00000285106\tTranscript\tsynonymous_variant\tsynonymous_variant\t1288/2936\t573/1971\t191/656\tK\taaG/aaA\trs533080894;COSV99497229\t\t-1\tCXXC1\tHGNC\tHGNC:24343\tprotein_coding\t\tCCDS11945.1\tENSP00000285106\tQ9P0U4.172\t\tUPI0000037D2E\tQ9P0U4-1\tNM_014593.3\t\tP1\t\t\t\t5/15\t\tPDB-ENSP_mappings:3qmb.A;PDB-ENSP_mappings:3qmc.A;PDB-ENSP_mappings:3qmd.A;PDB-ENSP_mappings:3qmg.A;PDB-ENSP_mappings:3qmh.A;PDB-ENSP_mappings:3qmi.A;PROSITE_profiles:PS51058;PANTHER:PTHR46174;Pfam:PF02008\t0.0006\t0.0\t0.0043\t0.0\t0.0\t0.0\t\t\t3.58e-05\t0.0\t0.0002314\t0.0\t0.0\t0.0\t0.0\t0.0001629\t0.0\t0.0043\tAMR\t4.7304998588515446e-05\t0.0\t0.0\t0.0004633920034393668\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0004633920034393668\tamr\t\t0;1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t0;1\t\tAACTTCTTCAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;varscan2\nDCC\t1630\tBI\tGRCh38\tchr18\t53499321\t53499321\t+\tNonsense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.3922C>T\tp.Gln1308Ter\tp.Q1308*\tENST00000442544\t27/29\t67\t56\t11\t113\t\t\tDCC,stop_gained,p.Q1308*,ENST00000442544,NM_005215.4,c.3922C>T,HIGH,YES,,,1;DCC,stop_gained,p.Q1285*,ENST00000412726,,c.3853C>T,HIGH,,,,1;DCC,stop_gained,p.Q941*,ENST00000581580,,c.2821C>T,HIGH,,,,1;DCC,non_coding_transcript_exon_variant,,ENST00000579702,,n.7C>T,MODIFIER,,,,1;LINC01917,intron_variant,,ENST00000582064,,n.218+5902G>A,MODIFIER,,,,-1;LINC01917,intron_variant,,ENST00000650275,,n.458+5902G>A,MODIFIER,,,,-1;LINC01917,intron_variant,,ENST00000671412,,n.713+5902G>A,MODIFIER,,,,-1\tT\tENSG00000187323\tENST00000442544\tTranscript\tstop_gained\tstop_gained\t4513/10181\t3922/4344\t1308/1447\tQ/*\tCaa/Taa\tCOSV101473539\t\t1\tDCC\tHGNC\tHGNC:2701\tprotein_coding\tYES\tCCDS11952.1\tENSP00000389140\tP43146.196\t\tUPI00001AEDC6\t\tNM_005215.4\tNM_005215.4\tP1\t\t\t\t27/29\t\tPfam:PF06583;PANTHER:PTHR44170;PANTHER:PTHR44170:SF8;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tHIGH\t1\tSNV\t1\t\t1\t1\tCTACCCAACAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNEDD4L\t23327\tBI\tGRCh38\tchr18\t58341138\t58341138\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs1312844888\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1226G>A\tp.Arg409Gln\tp.R409Q\tENST00000400345\t14/31\t25\t16\t9\t13\t\t\tNEDD4L,missense_variant,p.R409Q,ENST00000400345,NM_001144967.3,c.1226G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.826),1;NEDD4L,missense_variant,p.R288Q,ENST00000456986,NM_001144964.1&NM_001144965.2,c.863G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.826),1;NEDD4L,missense_variant,p.R389Q,ENST00000382850,NM_015277.6,c.1166G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.63),1;NEDD4L,missense_variant,p.R382Q,ENST00000675147,,c.1145G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.682),1;NEDD4L,missense_variant,p.R268Q,ENST00000675801,,c.803G>A,MODERATE,,deleterious(0.03),probably_damaging(0.979),1;NEDD4L,missense_variant,p.R268Q,ENST00000456173,NM_001144970.3,c.803G>A,MODERATE,,deleterious(0.03),probably_damaging(0.979),1;NEDD4L,missense_variant,p.R268Q,ENST00000676226,,c.803G>A,MODERATE,,deleterious(0.03),probably_damaging(0.979),1;NEDD4L,missense_variant,p.R268Q,ENST00000675502,,c.803G>A,MODERATE,,deleterious(0.03),probably_damaging(0.979),1;NEDD4L,missense_variant,p.R268Q,ENST00000675865,,c.803G>A,MODERATE,,deleterious(0.03),probably_damaging(0.979),1;NEDD4L,missense_variant,p.R364Q,ENST00000675221,,c.1091G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.682),1;NEDD4L,missense_variant,p.R376Q,ENST00000676223,,c.1127G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.682),1;NEDD4L,missense_variant,p.R389Q,ENST00000676024,,c.1166G>A,MODERATE,,tolerated(0.16),benign(0.136),1;NEDD4L,missense_variant,p.R268Q,ENST00000674517,,c.803G>A,MODERATE,,deleterious(0.03),probably_damaging(0.979),1;NEDD4L,missense_variant,p.R688Q,ENST00000635997,,c.2063G>A,MODERATE,YES,deleterious(0.04),probably_damaging(0.964),1;NEDD4L,missense_variant,p.R401Q,ENST00000357895,NM_001144968.2,c.1202G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.63),1;NEDD4L,missense_variant,p.R268Q,ENST00000435432,NM_001144971.2,c.803G>A,MODERATE,,deleterious(0.03),probably_damaging(0.979),1;NEDD4L,missense_variant,p.R381Q,ENST00000586263,NM_001144969.2,c.1142G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.733),1;NEDD4L,missense_variant,p.R288Q,ENST00000431212,NM_001144966.3,c.863G>A,MODERATE,,deleterious(0.03),possibly_damaging(0.826),1;NEDD4L,intron_variant,,ENST00000256830,,c.1066-1768G>A,MODIFIER,,,,1;NEDD4L,intron_variant,,ENST00000356462,NM_001243960.2,c.1066-540G>A,MODIFIER,,,,1;NEDD4L,intron_variant,,ENST00000587881,,c.567+7246G>A,MODIFIER,,,,1;NEDD4L,intron_variant,,ENST00000589054,,c.49-49508G>A,MODIFIER,,,,1;NEDD4L,non_coding_transcript_exon_variant,,ENST00000674636,,n.1306G>A,MODIFIER,,,,1;NEDD4L,non_coding_transcript_exon_variant,,ENST00000674856,,n.964G>A,MODIFIER,,,,1;NEDD4L,3_prime_UTR_variant,,ENST00000674845,,c.*1672G>A,MODIFIER,,,,1;NEDD4L,non_coding_transcript_exon_variant,,ENST00000675434,,n.1030G>A,MODIFIER,,,,1;NEDD4L,non_coding_transcript_exon_variant,,ENST00000590638,,n.180G>A,MODIFIER,,,,1;NEDD4L,downstream_gene_variant,,ENST00000676251,,,MODIFIER,,,,1\tA\tENSG00000049759\tENST00000400345\tTranscript\tmissense_variant\tmissense_variant\t1661/8633\t1226/2928\t409/975\tR/Q\tcGa/cAa\trs1312844888;COSV99896534\t\t1\tNEDD4L\tHGNC\tHGNC:7728\tprotein_coding\t\tCCDS45872.1\tENSP00000383199\tQ96PU5.183\t\tUPI000058E3AE\tQ96PU5-1\tNM_001144967.3\tNM_001144967.3\tP4\t\tdeleterious(0.03)\tpossibly_damaging(0.826)\t14/31\t\tPDB-ENSP_mappings:2lb2.A;PDB-ENSP_mappings:2lty.A;PROSITE_patterns:PS01159;PANTHER:PTHR11254:SF310;PANTHER:PTHR11254;PROSITE_profiles:PS50020;Superfamily:SSF51045;SMART:SM00456;Pfam:PF00397;Gene3D:2.20.70.10;PIRSF:PIRSF001569;CDD:cd00201\t\t\t\t\t\t\t\t\t8.097e-06\t6.559e-05\t0.0\t0.0\t0.0\t0.0\t8.918e-06\t0.0\t0.0\t6.559e-05\tgnomAD_AFR\t6.763340024917852e-06\t0.0\t0.0\t6.626910180784762e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t0;1\t1\tCAATCGAACCA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCDH7\t1005\tBI\tGRCh38\tchr18\t65809935\t65809935\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.442G>A\tp.Asp148Asn\tp.D148N\tENST00000323011\t3/12\t79\t65\t14\t115\t\t\tCDH7,missense_variant,p.D148N,ENST00000397968,NM_001362438.2&NM_004361.5,c.442G>A,MODERATE,YES,deleterious(0),probably_damaging(0.991),1;CDH7,missense_variant,p.D148N,ENST00000536984,NM_001317214.3,c.442G>A,MODERATE,,deleterious(0),probably_damaging(0.991),1;CDH7,missense_variant,p.D148N,ENST00000323011,NM_033646.3,c.442G>A,MODERATE,,deleterious(0),probably_damaging(0.991),1\tA\tENSG00000081138\tENST00000323011\tTranscript\tmissense_variant\tmissense_variant\t767/2728\t442/2358\t148/785\tD/N\tGac/Aac\tCOSV59887317\t\t1\tCDH7\tHGNC\tHGNC:1766\tprotein_coding\t\tCCDS11993.1\tENSP00000319166\tQ9ULB5.156\t\tUPI000013D269\t\tNM_033646.3\t\tP1\t\tdeleterious(0)\tprobably_damaging(0.991)\t3/12\t\tGene3D:2.60.40.60;PROSITE_profiles:PS50268;PANTHER:PTHR24027;PANTHER:PTHR24027:SF91;SMART:SM00112;Superfamily:SSF49313;Superfamily:SSF49313;CDD:cd11304\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tTCAACGACAAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF407\t55628\tBI\tGRCh38\tchr18\t74633143\t74633143\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2124G>C\tp.Lys708Asn\tp.K708N\tENST00000299687\t1/8\t29\t21\t8\t30\t\t\tZNF407,missense_variant,p.K708N,ENST00000299687,NM_017757.2,c.2124G>C,MODERATE,YES,deleterious(0.03),probably_damaging(0.997),1;ZNF407,missense_variant,p.K708N,ENST00000577538,NM_001146189.1,c.2124G>C,MODERATE,,deleterious(0.03),probably_damaging(0.998),1;ZNF407,missense_variant,p.K708N,ENST00000582337,,c.2124G>C,MODERATE,,deleterious(0),probably_damaging(0.995),1;ZNF407,missense_variant,p.K708N,ENST00000309902,NM_001146190.1,c.2124G>C,MODERATE,,deleterious(0),probably_damaging(0.995),1\tC\tENSG00000215421\tENST00000299687\tTranscript\tmissense_variant\tmissense_variant\t2124/7948\t2124/6747\t708/2248\tK/N\taaG/aaC\tCOSV99996740\t\t1\tZNF407\tHGNC\tHGNC:19904\tprotein_coding\tYES\tCCDS45885.1\tENSP00000299687\tQ9C0G0.147\t\tUPI0000F58ED1\tQ9C0G0-1\tNM_017757.2\t\tP4\t\tdeleterious(0.03)\tprobably_damaging(0.997)\t1/8\t\tSMART:SM00355\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tTGTAAGAAGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCTDP1\t9150\tBI\tGRCh38\tchr18\t79717674\t79717674\t+\tSplice_Region\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2208G>A\tp.Gln736=\tp.Q736=\tENST00000613122\t9/13\t76\t51\t25\t104\t\t\tCTDP1,splice_region_variant,p.Q736=,ENST00000613122,NM_004715.5,c.2208G>A,LOW,YES,,,1;CTDP1,splice_region_variant,p.Q736=,ENST00000075430,NM_048368.4,c.2208G>A,LOW,,,,1;CTDP1,splice_region_variant,p.Q617=,ENST00000299543,NM_001202504.1,c.1851G>A,LOW,,,,1;CTDP1,splice_region_variant,p.Q668=,ENST00000591598,NM_001318511.2,c.2004G>A,LOW,,,,1\tA\tENSG00000060069\tENST00000613122\tTranscript\tsplice_region_variant\tsplice_region_variant;synonymous_variant\t2353/3744\t2208/2886\t736/961\tQ\tcaG/caA\tCOSV50010192;COSV99311103\t\t1\tCTDP1\tHGNC\tHGNC:2498\tprotein_coding\tYES\tCCDS12017.1\tENSP00000484525\tQ9Y5B0.190\t\tUPI000013C57B\tQ9Y5B0-1\tNM_004715.5\tNM_004715.5\tP3\t\t\t\t9/13\t\tMobiDB_lite:mobidb-lite;PANTHER:PTHR23081:SF0;PANTHER:PTHR23081;Pfam:PF09309\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1;1\t1\tGCACAGAGGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nGRIN3B\t116444\tBI\tGRCh38\tchr19\t1005182\t1005182\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1681G>A\tp.Asp561Asn\tp.D561N\tENST00000234389\t3/9\t119\t95\t24\t81\t\t\tGRIN3B,missense_variant,p.D561N,ENST00000234389,NM_138690.3,c.1681G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;TMEM259,downstream_gene_variant,,ENST00000333175,NM_033420.4,,MODIFIER,,,,-1;TMEM259,downstream_gene_variant,,ENST00000356663,NM_001033026.2,,MODIFIER,YES,,,-1;TMEM259,downstream_gene_variant,,ENST00000592590,,,MODIFIER,,,,-1;GRIN3B,non_coding_transcript_exon_variant,,ENST00000588335,,n.431G>A,MODIFIER,,,,1;TMEM259,downstream_gene_variant,,ENST00000586704,,,MODIFIER,,,,-1;TMEM259,downstream_gene_variant,,ENST00000592052,,,MODIFIER,,,,-1;TMEM259,downstream_gene_variant,,ENST00000592618,,,MODIFIER,,,,-1;TMEM259,downstream_gene_variant,,ENST00000593068,,,MODIFIER,,,,-1;AC004528.1,upstream_gene_variant,,ENST00000588380,,,MODIFIER,YES,,,-1\tA\tENSG00000116032\tENST00000234389\tTranscript\tmissense_variant\tmissense_variant\t1700/3281\t1681/3132\t561/1043\tD/N\tGac/Aac\tCOSV99312908\t\t1\tGRIN3B\tHGNC\tHGNC:16768\tprotein_coding\tYES\tCCDS32861.1\tENSP00000234389\tO60391.159\t\tUPI000004064B\t\tNM_138690.3\tNM_138690.3\tP1\t\tdeleterious(0)\tprobably_damaging(0.999)\t3/9\t\tGene3D:3.40.190.10;PANTHER:PTHR18966;PANTHER:PTHR18966:SF364;SMART:SM00079;Superfamily:SSF53850;CDD:cd13720\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCACGGGACACG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nDENND1C\t79958\tBI\tGRCh38\tchr19\t6476952\t6476952\t+\tSilent\tSNP\tG\tG\tA\trs756970545\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.583C>T\tp.Leu195=\tp.L195=\tENST00000381480\t10/23\t73\t41\t32\t57\t\t\tDENND1C,synonymous_variant,p.L195=,ENST00000381480,NM_024898.4,c.583C>T,LOW,YES,,,-1;DENND1C,synonymous_variant,p.L151=,ENST00000543576,NM_001290331.2,c.451C>T,LOW,,,,-1;DENND1C,downstream_gene_variant,,ENST00000588421,,,MODIFIER,,,,-1;DENND1C,downstream_gene_variant,,ENST00000590173,,,MODIFIER,,,,-1;DENND1C,downstream_gene_variant,,ENST00000590473,,,MODIFIER,,,,-1;DENND1C,downstream_gene_variant,,ENST00000591030,,,MODIFIER,,,,-1;DENND1C,synonymous_variant,p.L151=,ENST00000590867,,c.451C>T,LOW,,,,-1;DENND1C,non_coding_transcript_exon_variant,,ENST00000592543,,n.599C>T,MODIFIER,,,,-1;DENND1C,non_coding_transcript_exon_variant,,ENST00000589491,,n.441C>T,MODIFIER,,,,-1;DENND1C,non_coding_transcript_exon_variant,,ENST00000588988,,n.341C>T,MODIFIER,,,,-1;DENND1C,downstream_gene_variant,,ENST00000586046,,,MODIFIER,,,,-1;DENND1C,upstream_gene_variant,,ENST00000590444,,,MODIFIER,,,,-1;DENND1C,upstream_gene_variant,,ENST00000590818,,,MODIFIER,,,,-1\tA\tENSG00000205744\tENST00000381480\tTranscript\tsynonymous_variant\tsynonymous_variant\t675/2795\t583/2406\t195/801\tL\tCtg/Ttg\trs756970545;COSV101200253;COSV67373704\t\t-1\tDENND1C\tHGNC\tHGNC:26225\tprotein_coding\tYES\tCCDS45938.1\tENSP00000370889\tQ8IV53.116\t\tUPI000007469C\tQ8IV53-1\tNM_024898.4\tNM_024898.4\tP1\t\t\t\t10/23\t\tGene3D:3.40.50.11500;Pfam:PF02141;PROSITE_profiles:PS50211;PANTHER:PTHR13196;PANTHER:PTHR13196:SF25;SMART:SM00799\t\t\t\t\t\t\t\t\t4.021e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.879e-06\t0.0\t0.0\t8.879e-06\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t0;1;1\t\tCACCAGCTCCG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCERS4\t79603\tBI\tGRCh38\tchr19\t8254517\t8254517\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.192G>A\tp.Leu64=\tp.L64=\tENST00000251363\t4/12\t61\t45\t16\t42\t\t\tCERS4,synonymous_variant,p.L13=,ENST00000558331,,c.39G>A,LOW,,,,1;CERS4,synonymous_variant,p.L64=,ENST00000251363,NM_024552.3,c.192G>A,LOW,YES,,,1;CERS4,synonymous_variant,p.L64=,ENST00000559450,,c.192G>A,LOW,,,,1;CERS4,synonymous_variant,p.L64=,ENST00000559336,,c.192G>A,LOW,,,,1;CERS4,synonymous_variant,p.L64=,ENST00000561053,,c.192G>A,LOW,,,,1;CERS4,synonymous_variant,p.L64=,ENST00000558877,,c.192G>A,LOW,,,,1;CERS4,synonymous_variant,p.L64=,ENST00000558268,,c.192G>A,LOW,,,,1;CERS4,synonymous_variant,p.L64=,ENST00000561008,,c.192G>A,LOW,,,,1;CERS4,downstream_gene_variant,,ENST00000560412,,,MODIFIER,,,,1;CERS4,non_coding_transcript_exon_variant,,ENST00000595722,,n.521G>A,MODIFIER,,,,1;CERS4,non_coding_transcript_exon_variant,,ENST00000557925,,n.743G>A,MODIFIER,,,,1;CERS4,non_coding_transcript_exon_variant,,ENST00000558501,,n.240G>A,MODIFIER,,,,1\tA\tENSG00000090661\tENST00000251363\tTranscript\tsynonymous_variant\tsynonymous_variant\t475/1780\t192/1185\t64/394\tL\tctG/ctA\tCOSV99250821\t\t1\tCERS4\tHGNC\tHGNC:23747\tprotein_coding\tYES\tCCDS12197.1\tENSP00000251363\tQ9HA82.162\t\tUPI000013CCFB\t\tNM_024552.3\tNM_024552.3\tP2\t\t\t\t4/12\t\tPANTHER:PTHR12560:SF6;PANTHER:PTHR12560;PIRSF:PIRSF005225\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tCCCCTGAGCCG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nACTL9\t284382\tBI\tGRCh38\tchr19\t8698376\t8698376\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs534855327\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.326C>T\tp.Thr109Met\tp.T109M\tENST00000324436\t1/1\t57\t37\t20\t63\t\t\tACTL9,missense_variant,p.T109M,ENST00000324436,NM_178525.5,c.326C>T,MODERATE,YES,tolerated(0.09),benign(0.143),-1;ACTL9,missense_variant,p.T109M,ENST00000612068,,c.326C>T,MODERATE,,tolerated(0.09),benign(0.143),-1;AC243312.1,upstream_gene_variant,,ENST00000623340,,,MODIFIER,YES,,,-1\tA\tENSG00000181786\tENST00000324436\tTranscript\tmissense_variant\tmissense_variant\t420/1396\t326/1251\t109/416\tT/M\taCg/aTg\trs534855327;COSV100185547\t\t-1\tACTL9\tHGNC\tHGNC:28494\tprotein_coding\tYES\tCCDS12207.1\tENSP00000316674\tQ8TC94.114\t\tUPI000000DB15\t\tNM_178525.5\tNM_178525.5\tP1\t\ttolerated(0.09)\tbenign(0.143)\t1/1\t\tCDD:cd00012;PANTHER:PTHR11937:SF194;PANTHER:PTHR11937;Gene3D:3.30.420.40;Pfam:PF00022;SMART:SM00268;Superfamily:SSF53067;Prints:PR00190\t\t\t\t\t\t\t\t\t1.706e-05\t0.0\t4.595e-05\t0.0\t0.0\t0.0001227\t0.0\t0.0\t0.0\t0.0001227\tgnomAD_FIN\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t\t\t0;1\t\tCCAGCGTCAGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nMUC16\t94025\tBI\tGRCh38\tchr19\t8937326\t8937326\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.33629C>T\tp.Ser11210Leu\tp.S11210L\tENST00000397910\t5/84\t32\t29\t3\t28\t\t\tMUC16,missense_variant,p.S11210L,ENST00000397910,NM_024690.2,c.33629C>T,MODERATE,YES,deleterious_low_confidence(0.04),probably_damaging(0.986),-1\tA\tENSG00000181143\tENST00000397910\tTranscript\tmissense_variant\tmissense_variant\t33833/43816\t33629/43524\t11210/14507\tS/L\ttCa/tTa\tCOSV101201647\t\t-1\tMUC16\tHGNC\tHGNC:15582\tprotein_coding\tYES\tCCDS54212.1\tENSP00000381008\tQ8WXI7.134\t\tUPI000065CA24\t\tNM_024690.2\t\tP1\t\tdeleterious_low_confidence(0.04)\tprobably_damaging(0.986)\t5/84\t\tPANTHER:PTHR14672\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t5\t\t1\t1\tCCAGTGAAGTC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nZNF266\t10781\tBI\tGRCh38\tchr19\t9414712\t9414712\t+\tMissense_Mutation\tSNP\tG\tG\tT\trs1334032824\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.213C>A\tp.Ser71Arg\tp.S71R\tENST00000588221\t9/9\t102\t58\t43\t66\t\t\tZNF266,missense_variant,p.S71R,ENST00000651268,NM_006631.3&NM_001370394.1&NM_001370399.1&NM_001370378.1&NM_001370400.1&NM_001370398.1&NM_001370377.1&NM_001370387.1&NM_001370386.1&NM_001370391.1&NM_001370383.1&NM_001370376.1&NM_001370397.1&NM_001370393.1&NM_001370395.1&NM_001370389.1&NM_001370392.1,c.213C>A,MODERATE,,tolerated(0.23),benign(0.243),-1;ZNF266,missense_variant,p.S138R,ENST00000592904,NM_001370385.1&NM_001370384.1&NM_001370375.1&NM_001370374.1,c.414C>A,MODERATE,YES,tolerated(0.29),benign(0.049),-1;ZNF266,missense_variant,p.S71R,ENST00000588221,NM_001370388.1&NM_001370382.1&NM_001370380.1&NM_001370390.1&NM_001370381.1,c.213C>A,MODERATE,,tolerated(0.23),benign(0.243),-1;ZNF266,missense_variant,p.S71R,ENST00000590306,,c.213C>A,MODERATE,,tolerated(0.23),benign(0.243),-1;ZNF266,missense_variant,p.S71R,ENST00000588933,NM_001271314.1&NM_001370379.1&NM_001370396.1,c.213C>A,MODERATE,,tolerated(0.23),benign(0.243),-1;ZNF266,missense_variant,p.S71R,ENST00000592292,,c.213C>A,MODERATE,,tolerated(0.23),benign(0.243),-1;ZNF266,non_coding_transcript_exon_variant,,ENST00000648978,,n.2290C>A,MODIFIER,,,,-1;ZNF266,non_coding_transcript_exon_variant,,ENST00000591213,,n.756C>A,MODIFIER,,,,-1\tT\tENSG00000174652\tENST00000588221\tTranscript\tmissense_variant\tmissense_variant\t1389/3503\t213/1650\t71/549\tS/R\tagC/agA\trs1334032824;COSV100749445\t\t-1\tZNF266\tHGNC\tHGNC:13059\tprotein_coding\t\tCCDS12213.1\tENSP00000468491\tQ14584.186\tA0A024R7B6.51\tUPI00001D4705\t\tNM_001370388.1;NM_001370382.1;NM_001370380.1;NM_001370390.1;NM_001370381.1\t\t\t\ttolerated(0.23)\tbenign(0.243)\t9/9\t\tPANTHER:PTHR24381;PANTHER:PTHR24381:SF149\t\t\t\t\t\t\t\t\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\tgnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t2\t\t0;1\t\tTTGTGGCTTCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nFBXL12\t54850\tBI\tGRCh38\tchr19\t9811208\t9811208\t+\tSilent\tSNP\tG\tG\tA\trs760302713\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.669C>T\tp.Ile223=\tp.I223=\tENST00000247977\t3/3\t64\t46\t17\t46\t\t\tFBXL12,synonymous_variant,p.I223=,ENST00000247977,NM_001316936.2&NM_017703.3,c.669C>T,LOW,YES,,,-1;FBXL12,synonymous_variant,p.I170=,ENST00000591009,NM_001316941.2,c.510C>T,LOW,,,,-1;FBXL12,synonymous_variant,p.I170=,ENST00000585379,NM_001316940.2&NM_001316937.2&NM_001316939.2&NM_001316942.2&NM_001316938.2,c.510C>T,LOW,,,,-1;FBXL12,3_prime_UTR_variant,,ENST00000589626,,c.*545C>T,MODIFIER,,,,-1;FBXL12,3_prime_UTR_variant,,ENST00000588922,,c.*499C>T,MODIFIER,,,,-1;FBXL12,3_prime_UTR_variant,,ENST00000586651,,c.*521C>T,MODIFIER,,,,-1;FBXL12,downstream_gene_variant,,ENST00000586469,,,MODIFIER,,,,-1;FBXL12,downstream_gene_variant,,ENST00000590277,,,MODIFIER,,,,-1;FBXL12,downstream_gene_variant,,ENST00000592067,,,MODIFIER,,,,-1;FBXL12,3_prime_UTR_variant,,ENST00000589438,,c.*723C>T,MODIFIER,,,,-1;FBXL12,3_prime_UTR_variant,,ENST00000592732,,c.*588C>T,MODIFIER,,,,-1;FBXL12,downstream_gene_variant,,ENST00000590808,,,MODIFIER,,,,-1\tA\tENSG00000127452\tENST00000247977\tTranscript\tsynonymous_variant\tsynonymous_variant\t935/1873\t669/981\t223/326\tI\tatC/atT\trs760302713;COSV56114958;COSV99928132\t\t-1\tFBXL12\tHGNC\tHGNC:13611\tprotein_coding\tYES\tCCDS12218.1\tENSP00000247977\tQ9NXK8.155\t\tUPI000006EBD0\tQ9NXK8-1\tNM_001316936.2;NM_017703.3\tNM_017703.3\tP1\t\t\t\t3/3\t\tPANTHER:PTHR16134:SF3;PANTHER:PTHR16134;Gene3D:3.80.10.10;Superfamily:SSF52047\t\t\t\t\t\t\t\t\t4.015e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.92e-06\t0.0\t0.0\t8.92e-06\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t0;1;1\t\tCGGCTGATGGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nATG4D\t84971\tBI\tGRCh38\tchr19\t10552926\t10552926\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1284C>T\tp.Phe428=\tp.F428=\tENST00000309469\t10/10\t161\t118\t42\t119\t\t\tATG4D,synonymous_variant,p.F428=,ENST00000309469,NM_001281504.2&NM_032885.6,c.1284C>T,LOW,YES,,,1;ATG4D,synonymous_variant,p.F131=,ENST00000588972,,c.393C>T,LOW,,,,1;ATG4D,synonymous_variant,p.F53=,ENST00000585437,,c.159C>T,LOW,,,,1;KRI1,downstream_gene_variant,,ENST00000312962,NM_023008.5,,MODIFIER,,,,-1;KRI1,downstream_gene_variant,,ENST00000539027,,,MODIFIER,,,,-1;ATG4D,downstream_gene_variant,,ENST00000586863,,,MODIFIER,,,,1;ATG4D,downstream_gene_variant,,ENST00000587256,,,MODIFIER,,,,1;KRI1,downstream_gene_variant,,ENST00000652042,,,MODIFIER,YES,,,-1;MIR1238,downstream_gene_variant,,ENST00000408483,,,MODIFIER,YES,,,1;RNU7-140P,upstream_gene_variant,,ENST00000459546,,,MODIFIER,YES,,,-1;KRI1,downstream_gene_variant,,ENST00000618579,,,MODIFIER,,,,-1;ATG4D,3_prime_UTR_variant,,ENST00000586417,,c.*875C>T,MODIFIER,,,,1;ATG4D,3_prime_UTR_variant,,ENST00000588667,,c.*320C>T,MODIFIER,,,,1;ATG4D,3_prime_UTR_variant,,ENST00000588857,,c.*235C>T,MODIFIER,,,,1;ATG4D,3_prime_UTR_variant,,ENST00000589753,,c.*235C>T,MODIFIER,,,,1;KRI1,downstream_gene_variant,,ENST00000478863,,,MODIFIER,,,,-1;KRI1,downstream_gene_variant,,ENST00000536689,,,MODIFIER,,,,-1;KRI1,downstream_gene_variant,,ENST00000536714,,,MODIFIER,,,,-1;KRI1,downstream_gene_variant,,ENST00000537363,,,MODIFIER,,,,-1;KRI1,downstream_gene_variant,,ENST00000537433,,,MODIFIER,,,,-1;KRI1,downstream_gene_variant,,ENST00000543842,,,MODIFIER,,,,-1;ATG4D,downstream_gene_variant,,ENST00000585752,,,MODIFIER,,,,1;ATG4D,downstream_gene_variant,,ENST00000590096,,,MODIFIER,,,,1;KRI1,downstream_gene_variant,,ENST00000612875,,,MODIFIER,,,,-1\tT\tENSG00000130734\tENST00000309469\tTranscript\tsynonymous_variant\tsynonymous_variant\t1471/1963\t1284/1425\t428/474\tF\tttC/ttT\tCOSV100470447\t\t1\tATG4D\tHGNC\tHGNC:20789\tprotein_coding\tYES\tCCDS12241.1\tENSP00000311318\tQ86TL0.140\t\tUPI000000DCA0\tQ86TL0-1\tNM_001281504.2;NM_032885.6\tNM_032885.6\tP1\t\t\t\t10/10\t\tPANTHER:PTHR22624;PANTHER:PTHR22624:SF36;Superfamily:SSF54001\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tATGTTCACCCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nWDR83\t84292\tBI\tGRCh38\tchr19\t12670566\t12670566\t+\tMissense_Mutation\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.334G>T\tp.Val112Leu\tp.V112L\tENST00000418543\t6/11\t471\t395\t76\t319\t\t\tWDR83,missense_variant,p.V112L,ENST00000418543,NM_001099737.3&NM_032332.4,c.334G>T,MODERATE,YES,deleterious(0.01),possibly_damaging(0.832),1;WDR83,missense_variant,p.V15L,ENST00000547797,,c.43G>T,MODERATE,,deleterious(0),possibly_damaging(0.754),1;MAN2B1,upstream_gene_variant,,ENST00000221363,NM_001173498.1,,MODIFIER,,,,-1;WDR83OS,upstream_gene_variant,,ENST00000222190,,,MODIFIER,,,,-1;MAN2B1,upstream_gene_variant,,ENST00000456935,NM_000528.4,,MODIFIER,YES,,,-1;MAN2B1,upstream_gene_variant,,ENST00000486847,,,MODIFIER,,,,-1;WDR83OS,upstream_gene_variant,,ENST00000596731,NM_016145.4,,MODIFIER,YES,,,-1;AC010422.5,upstream_gene_variant,,ENST00000597961,,,MODIFIER,YES,,,-1;WDR83OS,upstream_gene_variant,,ENST00000598732,,,MODIFIER,,,,-1;MAN2B1,upstream_gene_variant,,ENST00000598876,,,MODIFIER,,,,-1;MAN2B1,upstream_gene_variant,,ENST00000596512,,,MODIFIER,,,,-1;WDR83,missense_variant,p.V112L,ENST00000547481,,c.334G>T,MODERATE,,deleterious(0),benign(0.081),1;AC010422.8,3_prime_UTR_variant,,ENST00000648033,,c.*2772C>A,MODIFIER,YES,,,-1;WDR83,3_prime_UTR_variant,,ENST00000548381,,c.*101G>T,MODIFIER,,,,1;WDR83,3_prime_UTR_variant,,ENST00000553179,,c.*145G>T,MODIFIER,,,,1;WDR83,non_coding_transcript_exon_variant,,ENST00000546754,,n.747G>T,MODIFIER,,,,1;WDR83,non_coding_transcript_exon_variant,,ENST00000551329,,n.439G>T,MODIFIER,,,,1;WDR83,non_coding_transcript_exon_variant,,ENST00000550939,,n.494G>T,MODIFIER,,,,1;WDR83,intron_variant,,ENST00000425834,,c.195+281G>T,MODIFIER,,,,1;WDR83,intron_variant,,ENST00000547255,,n.634+281G>T,MODIFIER,,,,1;MAN2B1,upstream_gene_variant,,ENST00000466794,,,MODIFIER,,,,-1;WDR83,upstream_gene_variant,,ENST00000552700,,,MODIFIER,,,,1;MAN2B1,upstream_gene_variant,,ENST00000600281,,,MODIFIER,,,,-1;AC010422.7,intron_variant,,ENST00000600694,,n.348+110C>A,MODIFIER,YES,,,-1\tT\tENSG00000123154\tENST00000418543\tTranscript\tmissense_variant\tmissense_variant\t676/1450\t334/948\t112/315\tV/L\tGtg/Ttg\tCOSV99664028\t\t1\tWDR83\tHGNC\tHGNC:32672\tprotein_coding\tYES\tCCDS12275.1\tENSP00000402653\tQ9BRX9.157\t\tUPI000006DE5C\t\tNM_001099737.3;NM_032332.4\tNM_001099737.3\tP1\t\tdeleterious(0.01)\tpossibly_damaging(0.832)\t6/11\t\tGene3D:2.130.10.10;Pfam:PF00400;PROSITE_profiles:PS50082;PROSITE_profiles:PS50294;PANTHER:PTHR22842;PANTHER:PTHR22842:SF3;SMART:SM00320;Superfamily:SSF50978;CDD:cd00200\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tAGAAGGTGAAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nJUNB\t3726\tBI\tGRCh38\tchr19\t12792488\t12792488\t+\tSilent\tSNP\tC\tC\tT\trs1226993652\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.717C>T\tp.Phe239=\tp.F239=\tENST00000302754\t1/1\t18\t13\t5\t12\t\t\tJUNB,synonymous_variant,p.F239=,ENST00000302754,NM_002229.3,c.717C>T,LOW,YES,,,1;PRDX2,downstream_gene_variant,,ENST00000301522,NM_005809.6,,MODIFIER,YES,,,-1;PRDX2,downstream_gene_variant,,ENST00000334482,,,MODIFIER,,,,-1;HOOK2,intron_variant,,ENST00000589765,,n.42-18263G>A,MODIFIER,,,,-1;HOOK2,non_coding_transcript_exon_variant,,ENST00000593143,,n.95G>A,MODIFIER,,,,-1;PRDX2,downstream_gene_variant,,ENST00000466174,,,MODIFIER,,,,-1;AC018761.2,upstream_gene_variant,,ENST00000585496,,,MODIFIER,YES,,,1\tT\tENSG00000171223\tENST00000302754\tTranscript\tsynonymous_variant\tsynonymous_variant\t1003/1830\t717/1044\t239/347\tF\tttC/ttT\trs1226993652;COSV100040347\t\t1\tJUNB\tHGNC\tHGNC:6205\tprotein_coding\tYES\tCCDS12280.1\tENSP00000303315\tP17275.209\tQ5U079.128\tUPI000012DACF\t\tNM_002229.3\tNM_002229.3\tP1\t\t\t\t1/1\t\tPfam:PF03957;PANTHER:PTHR11462;PANTHER:PTHR11462:SF37\t\t\t\t\t\t\t\t\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\tgnomAD_AFR;gnomAD_AMR;gnomAD_ASJ;gnomAD_EAS;gnomAD_FIN;gnomAD_NFE;gnomAD_OTH;gnomAD_SAS\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t\tSNV\t\t\t0;1\t\tACCTTCAAGGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nMAST1\t22983\tBI\tGRCh38\tchr19\t12874495\t12874495\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.4338G>A\tp.Lys1446=\tp.K1446=\tENST00000251472\t26/26\t44\t35\t9\t27\t\t\tMAST1,synonymous_variant,p.K1446=,ENST00000251472,NM_014975.3,c.4338G>A,LOW,YES,,,1;DNASE2,downstream_gene_variant,,ENST00000222219,NM_001375.3,,MODIFIER,YES,,,-1;DNASE2,downstream_gene_variant,,ENST00000592506,,,MODIFIER,,,,-1;HOOK2,upstream_gene_variant,,ENST00000589765,,,MODIFIER,,,,-1;MAST1,downstream_gene_variant,,ENST00000585791,,,MODIFIER,,,,1;DNASE2,downstream_gene_variant,,ENST00000586547,,,MODIFIER,,,,-1;DNASE2,downstream_gene_variant,,ENST00000588777,,,MODIFIER,,,,-1;MAST1,downstream_gene_variant,,ENST00000590553,,,MODIFIER,,,,1\tA\tENSG00000105613\tENST00000251472\tTranscript\tsynonymous_variant\tsynonymous_variant\t4396/4853\t4338/4713\t1446/1570\tK\taaG/aaA\tCOSV99263687\t\t1\tMAST1\tHGNC\tHGNC:19034\tprotein_coding\tYES\tCCDS32921.1\tENSP00000251472\tQ9Y2H9.173\t\tUPI000004A042\t\tNM_014975.3\tNM_014975.3\tP1\t\t\t\t26/26\t\tMobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t1\tGCTAAGGCTGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCC2D1A\t54862\tBI\tGRCh38\tchr19\t13912418\t13912418\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.292G>A\tp.Glu98Lys\tp.E98K\tENST00000318003\t3/29\t37\t24\t13\t37\t\t\tCC2D1A,missense_variant,p.E98K,ENST00000318003,NM_017721.5,c.292G>A,MODERATE,YES,deleterious(0.02),possibly_damaging(0.549),1;CC2D1A,missense_variant,p.E98K,ENST00000589606,,c.292G>A,MODERATE,,deleterious(0.02),possibly_damaging(0.84),1;CC2D1A,intron_variant,,ENST00000585896,,n.436-750G>A,MODIFIER,,,,1;CC2D1A,upstream_gene_variant,,ENST00000586955,,,MODIFIER,,,,1\tA\tENSG00000132024\tENST00000318003\tTranscript\tmissense_variant\tmissense_variant\t533/3581\t292/2856\t98/951\tE/K\tGag/Aag\tCOSV100528696\t\t1\tCC2D1A\tHGNC\tHGNC:30237\tprotein_coding\tYES\tCCDS42512.1\tENSP00000313601\tQ6P1N0.144\t\tUPI0000203524\tQ6P1N0-1\tNM_017721.5\tNM_017721.5\tP3\t\tdeleterious(0.02)\tpossibly_damaging(0.549)\t3/29\t\tPANTHER:PTHR13076;PANTHER:PTHR13076:SF8;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t1\tACTTGGAGGCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nKLHL26\t55295\tBI\tGRCh38\tchr19\t18668927\t18668927\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1530C>T\tp.Ile510=\tp.I510=\tENST00000300976\t3/3\t141\t109\t32\t94\t\t\tKLHL26,synonymous_variant,p.I510=,ENST00000300976,NM_001345982.2&NM_018316.3&NM_001345981.2,c.1530C>T,LOW,YES,,,1;KLHL26,intron_variant,,ENST00000599006,NM_001345984.2,c.406-315C>T,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000595182,NM_001345985.2,,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000595423,,,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000596843,NM_001345983.1,,MODIFIER,,,,1;KLHL26,downstream_gene_variant,,ENST00000600657,,,MODIFIER,,,,1\tT\tENSG00000167487\tENST00000300976\tTranscript\tsynonymous_variant\tsynonymous_variant\t1557/4351\t1530/1848\t510/615\tI\tatC/atT\tCOSV99963370\t\t1\tKLHL26\tHGNC\tHGNC:25623\tprotein_coding\tYES\tCCDS12384.1\tENSP00000300976\tQ53HC5.121\tA0A024R7N5.57\tUPI0000071AC2\t\tNM_001345982.2;NM_018316.3;NM_001345981.2\tNM_018316.3\tP1\t\t\t\t3/3\t\tPANTHER:PTHR45632:SF13;PANTHER:PTHR45632;Gene3D:2.120.10.80;PIRSF:PIRSF037037;Pfam:PF01344;SMART:SM00612;Superfamily:SSF117281\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tCGCATCTATGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF682\t91120\tBI\tGRCh38\tchr19\t20006721\t20006721\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.781G>C\tp.Glu261Gln\tp.E261Q\tENST00000397165\t4/4\t63\t49\t14\t54\t\t\tZNF682,missense_variant,p.E261Q,ENST00000397165,NM_033196.3,c.781G>C,MODERATE,,deleterious(0.01),probably_damaging(0.988),-1;ZNF682,missense_variant,p.E229Q,ENST00000397162,NM_001077349.1,c.685G>C,MODERATE,,deleterious(0.01),probably_damaging(0.988),-1;ZNF682,missense_variant,p.E229Q,ENST00000358523,,c.685G>C,MODERATE,,deleterious(0.01),probably_damaging(0.988),-1;ZNF682,missense_variant,p.E185Q,ENST00000595736,,c.553G>C,MODERATE,,deleterious(0.01),probably_damaging(0.988),-1;ZNF682,missense_variant,p.E267Q,ENST00000597972,,c.799G>C,MODERATE,YES,deleterious(0.01),benign(0.011),-1;ZNF682,intron_variant,,ENST00000594127,,c.122+420G>C,MODIFIER,,,,-1;ZNF682,intron_variant,,ENST00000596019,,c.227-9458G>C,MODIFIER,,,,-1;ZNF682,intron_variant,,ENST00000602079,,c.147-1974G>C,MODIFIER,,,,-1;ZNF682,downstream_gene_variant,,ENST00000593468,,,MODIFIER,,,,-1;ZNF682,downstream_gene_variant,,ENST00000601100,,,MODIFIER,,,,-1;ZNF682,non_coding_transcript_exon_variant,,ENST00000601365,,n.1468G>C,MODIFIER,,,,-1;ZNF682,downstream_gene_variant,,ENST00000595534,,,MODIFIER,,,,-1\tG\tENSG00000197124\tENST00000397165\tTranscript\tmissense_variant\tmissense_variant\t941/3244\t781/1497\t261/498\tE/Q\tGaa/Caa\tCOSV100653356\t\t-1\tZNF682\tHGNC\tHGNC:28857\tprotein_coding\t\tCCDS42533.1\tENSP00000380351\tO95780.155\t\tUPI000007275A\tO95780-1\tNM_033196.3\tNM_033196.3\tA2\t\tdeleterious(0.01)\tprobably_damaging(0.988)\t4/4\t\tGene3D:3.30.160.60;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24384;PANTHER:PTHR24384;PANTHER:PTHR24384:SF134;PANTHER:PTHR24384:SF134;SMART:SM00355;Superfamily:SSF57667;Superfamily:SSF57667\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t2\t\t1\t\tACATTCTTCAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF486\t90649\tBI\tGRCh38\tchr19\t20197678\t20197678\t+\tMissense_Mutation\tSNP\tC\tC\tT\trs548386025\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.968C>T\tp.Thr323Met\tp.T323M\tENST00000335117\t4/4\t58\t48\t10\t55\t\t\tZNF486,missense_variant,p.T323M,ENST00000335117,NM_052852.4,c.968C>T,MODERATE,YES,deleterious(0),possibly_damaging(0.501),1;AC011447.3,intron_variant,,ENST00000585498,,n.174-20869G>A,MODIFIER,,,,-1;AC011447.3,intron_variant,,ENST00000586657,,n.165+40610G>A,MODIFIER,,,,-1;AC011447.3,intron_variant,,ENST00000593655,,n.337+42822G>A,MODIFIER,,,,-1\tT\tENSG00000256229\tENST00000335117\tTranscript\tmissense_variant\tmissense_variant\t1085/3895\t968/1392\t323/463\tT/M\taCg/aTg\trs548386025;COSV58719232\t\t1\tZNF486\tHGNC\tHGNC:20807\tprotein_coding\tYES\tCCDS46029.1\tENSP00000335042\tQ96H40.139\t\tUPI00002376E8\t\tNM_052852.4\tNM_052852.4\tP1\t\tdeleterious(0)\tpossibly_damaging(0.501)\t4/4\t\tGene3D:3.30.160.60;Pfam:PF00096;PROSITE_profiles:PS50157;PANTHER:PTHR24384;PANTHER:PTHR24384;PANTHER:PTHR24384:SF95;PANTHER:PTHR24384:SF95;SMART:SM00355;Superfamily:SSF57667\t0.0002\t0.0\t0.0\t0.001\t0.0\t0.0\t\t\t0.0002362\t0.0\t0.001506\t0.0\t0.0001089\t0.0\t3.537e-05\t0.000165\t0.0\t0.001506\tgnomAD_AMR\t6.804479926358908e-05\t7.354740228038281e-05\t0.0\t0.0003335110086482018\t0.0\t0.00020644099276978523\t0.0\t0.0\t1.5470799553440884e-05\t0.0\t0.0\t0.0003335110086482018\tamr\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t0;1\t\tGTACACGTGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM993531;COSM993532\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nTSHZ3\t57616\tBI\tGRCh38\tchr19\t31277782\t31277782\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs1261231665\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2011C>T\tp.Pro671Ser\tp.P671S\tENST00000240587\t2/2\t83\t71\t12\t43\t\t\tTSHZ3,missense_variant,p.P671S,ENST00000240587,NM_020856.4,c.2011C>T,MODERATE,YES,tolerated(0.18),benign(0.058),-1;TSHZ3,intron_variant,,ENST00000651361,,n.64-34907C>T,MODIFIER,,,,-1;TSHZ3,downstream_gene_variant,,ENST00000560707,,,MODIFIER,,,,-1\tA\tENSG00000121297\tENST00000240587\tTranscript\tmissense_variant\tmissense_variant\t2228/5065\t2011/3246\t671/1081\tP/S\tCcc/Tcc\trs1261231665;COSV99552707\t\t-1\tTSHZ3\tHGNC\tHGNC:30700\tprotein_coding\tYES\tCCDS12421.2\tENSP00000240587\tQ63HK5.158\t\tUPI0000202000\t\tNM_020856.4\tNM_020856.4\tP1\t\ttolerated(0.18)\tbenign(0.058)\t2/2\t\tMobiDB_lite:mobidb-lite;PANTHER:PTHR12487;PANTHER:PTHR12487:SF5\t\t\t\t\t\t\t\t\t1.09e-05\t0.0\t0.0\t0.0\t6.143e-05\t0.0\t1.142e-05\t0.0\t0.0\t6.143e-05\tgnomAD_EAS\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t0;1\t\tGCTGGGGCTGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nWDR62\t284403\tBI\tGRCh38\tchr19\t36092796\t36092796\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs762688861\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.2318G>A\tp.Arg773Gln\tp.R773Q\tENST00000270301\t19/32\t250\t173\t77\t144\t\t\tWDR62,missense_variant,p.R773Q,ENST00000401500,NM_001083961.2,c.2318G>A,MODERATE,YES,tolerated(0.6),benign(0),1;WDR62,missense_variant,p.R773Q,ENST00000270301,NM_173636.5,c.2318G>A,MODERATE,,tolerated(0.6),benign(0),1;WDR62,3_prime_UTR_variant,,ENST00000587391,,c.*1008G>A,MODIFIER,,,,1\tA\tENSG00000075702\tENST00000270301\tTranscript\tmissense_variant\tmissense_variant\t2318/4632\t2318/4557\t773/1518\tR/Q\tcGg/cAg\trs762688861;COSV99544000\t\t1\tWDR62\tHGNC\tHGNC:24502\tprotein_coding\t\tCCDS33001.1\tENSP00000270301\tO43379.166\t\tUPI0000DBEE90\tO43379-1\tNM_173636.5\t\tA2\t\ttolerated(0.6)\tbenign(0)\t19/32\t\tGene3D:2.130.10.10;PANTHER:PTHR45589;PANTHER:PTHR45589:SF3;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite\t\t\t\t\t\t\t\t\t1.992e-05\t6.157e-05\t2.891e-05\t0.0\t0.0\t0.0\t8.826e-06\t0.0\t6.533e-05\t6.533e-05\tgnomAD_SAS\t2.028070048254449e-05\t4.8626301577314734e-05\t0.0\t6.628660048590973e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t4.8626301577314734e-05\tafr\tuncertain_significance\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t5\t\t1;1\t1\tGAAGCGGAGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nFBXO27\t126433\tBI\tGRCh38\tchr19\t39026908\t39026908\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.670G>C\tp.Asp224His\tp.D224H\tENST00000292853\t5/6\t303\t289\t14\t204\t\t\tFBXO27,missense_variant,p.D224H,ENST00000292853,NM_178820.5,c.670G>C,MODERATE,YES,tolerated(0.54),benign(0.014),-1;FBXO27,missense_variant,p.D224H,ENST00000509137,,c.670G>C,MODERATE,,tolerated(0.54),benign(0.014),-1;FBXO27,missense_variant,p.D223H,ENST00000600828,,c.667G>C,MODERATE,,tolerated(0.54),possibly_damaging(0.849),-1;FBXO27,missense_variant,p.D19H,ENST00000598394,,c.55G>C,MODERATE,,deleterious_low_confidence(0.01),benign(0.007),-1;FBXO27,downstream_gene_variant,,ENST00000593847,,,MODIFIER,,,,-1;FBXO27,non_coding_transcript_exon_variant,,ENST00000594770,,n.590G>C,MODIFIER,,,,-1;FBXO27,non_coding_transcript_exon_variant,,ENST00000595166,,n.388G>C,MODIFIER,,,,-1;AC010605.1,upstream_gene_variant,,ENST00000597303,,,MODIFIER,YES,,,1\tG\tENSG00000161243\tENST00000292853\tTranscript\tmissense_variant\tmissense_variant\t743/2315\t670/852\t224/283\tD/H\tGat/Cat\tCOSV99494762\t\t-1\tFBXO27\tHGNC\tHGNC:18753\tprotein_coding\tYES\tCCDS12527.1\tENSP00000292853\tQ8NI29.136\tA0A384MR61.10\tUPI0000073006\t\tNM_178820.5\tNM_178820.5\tP4\t\ttolerated(0.54)\tbenign(0.014)\t5/6\t\tPROSITE_profiles:PS51114;PANTHER:PTHR12125;PANTHER:PTHR12125:SF9;Pfam:PF04300;Gene3D:2.60.120.260;SMART:SM01198;Superfamily:SSF49785\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tGGGATCAGGCA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nSPTBN4\t57731\tBI\tGRCh38\tchr19\t40520106\t40520106\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.3609C>T\tp.Leu1203=\tp.L1203=\tENST00000352632\t16/36\t68\t52\t16\t45\t\t\tSPTBN4,synonymous_variant,p.L1203=,ENST00000598249,NM_020971.3,c.3609C>T,LOW,YES,,,1;SPTBN4,synonymous_variant,p.L1203=,ENST00000338932,,c.3609C>T,LOW,,,,1;SPTBN4,synonymous_variant,p.L1203=,ENST00000352632,,c.3609C>T,LOW,,,,1;SPTBN4,synonymous_variant,p.L1203=,ENST00000392025,,c.3609C>T,LOW,,,,1;SPTBN4,synonymous_variant,p.L1203=,ENST00000595535,,c.3609C>T,LOW,,,,1;SPTBN4,synonymous_variant,p.L595=,ENST00000597389,,c.1785C>T,LOW,,,,1\tT\tENSG00000160460\tENST00000352632\tTranscript\tsynonymous_variant\tsynonymous_variant\t3695/8676\t3609/7695\t1203/2564\tL\tctC/ctT\tCOSV100152083\t\t1\tSPTBN4\tHGNC\tHGNC:14896\tprotein_coding\t\tCCDS12559.1\tENSP00000263373\tQ9H254.178\t\tUPI0000135DBB\tQ9H254-1\t\t\tP2\t\t\t\t16/36\t\tGene3D:1.20.58.60;PIRSF:PIRSF002297;PANTHER:PTHR11915;PANTHER:PTHR11915:SF232;SMART:SM00150;Superfamily:SSF46966;CDD:cd00176\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t5\t\t1\t1\tCAGCTCTTCCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSPTBN4\t57731\tBI\tGRCh38\tchr19\t40557395\t40557395\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs201094636\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.5662G>A\tp.Val1888Met\tp.V1888M\tENST00000352632\t26/36\t143\t120\t22\t98\t\t\tSPTBN4,missense_variant,p.V1888M,ENST00000598249,NM_020971.3,c.5662G>A,MODERATE,YES,tolerated(0.22),probably_damaging(0.997),1;SPTBN4,missense_variant,p.V1888M,ENST00000338932,,c.5662G>A,MODERATE,,tolerated(0.22),possibly_damaging(0.835),1;SPTBN4,missense_variant,p.V1888M,ENST00000352632,,c.5662G>A,MODERATE,,tolerated(0.22),probably_damaging(0.997),1;SPTBN4,missense_variant,p.V1888M,ENST00000392025,,c.5662G>A,MODERATE,,tolerated(0.22),possibly_damaging(0.835),1;SPTBN4,missense_variant,p.V1888M,ENST00000595535,,c.5662G>A,MODERATE,,tolerated(0.22),probably_damaging(0.999),1;SPTBN4,missense_variant,p.V564M,ENST00000392023,NM_025213.3,c.1690G>A,MODERATE,,tolerated(0.22),possibly_damaging(0.887),1;SPTBN4,3_prime_UTR_variant,,ENST00000597389,,c.*1818G>A,MODIFIER,,,,1;SPTBN4,downstream_gene_variant,,ENST00000596900,,,MODIFIER,,,,1\tA\tENSG00000160460\tENST00000352632\tTranscript\tmissense_variant\tmissense_variant\t5748/8676\t5662/7695\t1888/2564\tV/M\tGtg/Atg\trs201094636;COSV100152084\t\t1\tSPTBN4\tHGNC\tHGNC:14896\tprotein_coding\t\tCCDS12559.1\tENSP00000263373\tQ9H254.178\t\tUPI0000135DBB\tQ9H254-1\t\t\tP2\t\ttolerated(0.22)\tprobably_damaging(0.997)\t26/36\t\tGene3D:1.20.58.1940;Pfam:PF00435;PIRSF:PIRSF002297;PANTHER:PTHR11915;PANTHER:PTHR11915:SF232;SMART:SM00150;Superfamily:SSF46966;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t1.89e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t3.104e-05\t0.0002013\t0.0\t0.0002013\tgnomAD_OTH\t6.7597698034660425e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.5430699932039715e-05\t0.0\t0.0\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t5\t\t0;1\t1\tTCCTCGTGTCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSHKBP1\t92799\tBI\tGRCh38\tchr19\t40590774\t40590775\t+\tFrame_Shift_Del\tDEL\tTG\tTG\t-\trs1397072034\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1815_1816del\tp.Cys605Ter\tp.C605*\tENST00000291842\t17/18\t230\t166\t64\t140\t\t\tSHKBP1,frameshift_variant,p.C605*,ENST00000291842,NM_138392.4,c.1815_1816del,HIGH,YES,,,1;SHKBP1,frameshift_variant,p.C580*,ENST00000600733,,c.1740_1741del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C508*,ENST00000600718,,c.1523_1524del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C175*,ENST00000597396,,c.525_526del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C148*,ENST00000600320,,c.443_444del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C206*,ENST00000602011,,c.616_617del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C160*,ENST00000593764,,c.480_481del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C73*,ENST00000594298,,c.218_219del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C62*,ENST00000595726,,c.185_186del,HIGH,,,,1;SHKBP1,frameshift_variant,p.C41*,ENST00000594862,,c.122_123del,HIGH,,,,1;LTBP4,upstream_gene_variant,,ENST00000204005,NM_003573.2,,MODIFIER,,,,1;SHKBP1,downstream_gene_variant,,ENST00000597649,,,MODIFIER,,,,1;SHKBP1,frameshift_variant,p.*130Sfs*95,ENST00000596163,,c.387_388del,HIGH,,,,1;SHKBP1,non_coding_transcript_exon_variant,,ENST00000594973,,n.1842_1843del,MODIFIER,,,,1;SHKBP1,non_coding_transcript_exon_variant,,ENST00000598201,,n.1572_1573del,MODIFIER,,,,1;SHKBP1,non_coding_transcript_exon_variant,,ENST00000599833,,n.731_732del,MODIFIER,,,,1;SHKBP1,non_coding_transcript_exon_variant,,ENST00000602239,,n.261_262del,MODIFIER,,,,1;LTBP4,upstream_gene_variant,,ENST00000599016,,,MODIFIER,,,,1;LTBP4,upstream_gene_variant,,ENST00000600026,,,MODIFIER,,,,1;SHKBP1,downstream_gene_variant,,ENST00000600791,,,MODIFIER,,,,1\t-\tENSG00000160410\tENST00000291842\tTranscript\tframeshift_variant\tframeshift_variant\t1840-1841/2341\t1813-1814/2124\t605/707\tC/X\tTGt/t\trs1397072034\t\t1\tSHKBP1\tHGNC\tHGNC:19214\tprotein_coding\tYES\tCCDS12560.1\tENSP00000291842\tQ8TBC3.151\t\tUPI0000036171\tQ8TBC3-1\tNM_138392.4\tNM_138392.4\tP1\t\t\t\t17/18\t\tPANTHER:PTHR15859:SF5;PANTHER:PTHR15859\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t2.02981991606066e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t4.6316301450133324e-05\t0.0\t0.0\t4.6316301450133324e-05\tnfe\t\t\t\t\t\t\t\t\t\tHIGH\t1\tdeletion\t1\t2\t\t\tGAACACTGTGAGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tpindel;varscan2\nCYP2A6\t1548\tBI\tGRCh38\tchr19\t40848653\t40848653\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.454G>A\tp.Glu152Lys\tp.E152K\tENST00000301141\t3/9\t109\t92\t17\t75\t\t\tCYP2A6,missense_variant,p.E152K,ENST00000301141,NM_000762.6,c.454G>A,MODERATE,YES,deleterious(0.01),benign(0.192),-1;CYP2A6,3_prime_UTR_variant,,ENST00000600495,,c.*266G>A,MODIFIER,,,,-1;CYP2A6,non_coding_transcript_exon_variant,,ENST00000596719,,n.305G>A,MODIFIER,,,,-1;AC008537.1,intron_variant,,ENST00000601627,,c.120-43338C>T,MODIFIER,YES,,,1;CYP2A6,upstream_gene_variant,,ENST00000599960,,,MODIFIER,,,,-1\tT\tENSG00000255974\tENST00000301141\tTranscript\tmissense_variant\tmissense_variant\t475/1761\t454/1485\t152/494\tE/K\tGag/Aag\tCOSV56534928\t\t-1\tCYP2A6\tHGNC\tHGNC:2610\tprotein_coding\tYES\tCCDS12568.1\tENSP00000301141\tP11509.220\t\tUPI0000157752\t\tNM_000762.6\tNM_000762.6\tP1\t\tdeleterious(0.01)\tbenign(0.192)\t3/9\t\tPANTHER:PTHR24300:SF297;PANTHER:PTHR24300;Pfam:PF00067;Gene3D:1.10.630.10;Superfamily:SSF48264\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t1\tCGCCTCCTCCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM4548716\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCYP2A7\t1549\tBI\tGRCh38\tchr19\t40881610\t40881610\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.322G>C\tp.Asp108His\tp.D108H\tENST00000301146\t2/9\t170\t154\t16\t130\t\t\tCYP2A7,missense_variant,p.D108H,ENST00000301146,NM_000764.2,c.322G>C,MODERATE,YES,tolerated(0.06),possibly_damaging(0.876),-1;CYP2A7,intron_variant,,ENST00000291764,NM_030589.2,c.190+411G>C,MODIFIER,,,,-1;CYP2A7,intron_variant,,ENST00000594332,,c.180+421G>C,MODIFIER,,,,-1;AC008537.1,intron_variant,,ENST00000601627,,c.120-10381C>G,MODIFIER,YES,,,1;CYP2A7,upstream_gene_variant,,ENST00000598264,,,MODIFIER,,,,-1;CYP2A7,upstream_gene_variant,,ENST00000602008,,,MODIFIER,,,,-1\tG\tENSG00000198077\tENST00000301146\tTranscript\tmissense_variant\tmissense_variant\t864/2281\t322/1485\t108/494\tD/H\tGac/Cac\tCOSV99394514\t\t-1\tCYP2A7\tHGNC\tHGNC:2611\tprotein_coding\tYES\tCCDS12569.1\tENSP00000301146\tP20853.177\t\tUPI000013E6D5\t\tNM_000764.2\t\tP1\t\ttolerated(0.06)\tpossibly_damaging(0.876)\t2/9\t\tPANTHER:PTHR24300;PANTHER:PTHR24300:SF297;Gene3D:1.10.630.10;Pfam:PF00067;Superfamily:SSF48264\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCCAGTCGAAGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nAXL\t558\tBI\tGRCh38\tchr19\t41237954\t41237954\t+\tNonsense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.794C>G\tp.Ser265Ter\tp.S265*\tENST00000301178\t7/20\t81\t61\t20\t53\t\t\tAXL,stop_gained,p.S265*,ENST00000301178,NM_021913.5,c.794C>G,HIGH,YES,,,1;AXL,stop_gained,p.S265*,ENST00000359092,NM_001699.6,c.794C>G,HIGH,,,,1;AXL,5_prime_UTR_variant,,ENST00000593513,NM_001278599.1,c.-11C>G,MODIFIER,,,,1;AXL,non_coding_transcript_exon_variant,,ENST00000599659,,n.808C>G,MODIFIER,,,,1\tG\tENSG00000167601\tENST00000301178\tTranscript\tstop_gained\tstop_gained\t964/4717\t794/2685\t265/894\tS/*\ttCa/tGa\tCOSV99997244\t\t1\tAXL\tHGNC\tHGNC:905\tprotein_coding\tYES\tCCDS12575.1\tENSP00000301178\tP30530.213\t\tUPI000014319B\tP30530-1\tNM_021913.5\tNM_021913.5\tP4\t\t\t\t7/20\t\tCDD:cd00063;Pfam:PF00041;Gene3D:2.60.40.10;SMART:SM00060;Superfamily:SSF49265;PROSITE_profiles:PS50853;PANTHER:PTHR24416;PANTHER:PTHR24416:SF323\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tHIGH\t1\tSNV\t1\t\t1\t1\tGCTGTCAGACG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nATP1A3\t478\tBI\tGRCh38\tchr19\t41981588\t41981588\t+\tMissense_Mutation\tSNP\tC\tC\tG\tnovel\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1390G>C\tp.Glu464Gln\tp.E464Q\tENST00000545399\t11/23\t84\t66\t18\t55\t\t\tATP1A3,missense_variant,p.E464Q,ENST00000545399,NM_001256214.2,c.1390G>C,MODERATE,YES,deleterious(0.05),benign(0.317),-1;ATP1A3,missense_variant,p.E451Q,ENST00000648268,NM_152296.5,c.1351G>C,MODERATE,,deleterious(0.05),possibly_damaging(0.687),-1;ATP1A3,missense_variant,p.E421Q,ENST00000602133,,c.1261G>C,MODERATE,,tolerated(0.05),possibly_damaging(0.687),-1;ATP1A3,missense_variant,p.E462Q,ENST00000543770,NM_001256213.1,c.1384G>C,MODERATE,,deleterious(0.05),possibly_damaging(0.677),-1;ATP1A3,downstream_gene_variant,,ENST00000473086,,,MODIFIER,,,,-1;ATP1A3,missense_variant,p.E451Q,ENST00000441343,,c.1351G>C,MODERATE,,tolerated_low_confidence(0.05),possibly_damaging(0.842),-1;AC010616.1,missense_variant,p.E451Q,ENST00000644613,,c.1351G>C,MODERATE,YES,deleterious(0.05),probably_damaging(0.999),-1;ATP1A3,downstream_gene_variant,,ENST00000485672,,,MODIFIER,,,,-1;ATP1A3,downstream_gene_variant,,ENST00000645448,,,MODIFIER,,,,-1\tG\tENSG00000105409\tENST00000545399\tTranscript\tmissense_variant\tmissense_variant\t1584/3628\t1390/3081\t464/1026\tE/Q\tGag/Cag\t\t\t-1\tATP1A3\tHGNC\tHGNC:801\tprotein_coding\tYES\tCCDS58664.1\tENSP00000444688\tP13637.220\t\tUPI0001914BDE\tP13637-3\tNM_001256214.2\t\tA1\t\tdeleterious(0.05)\tbenign(0.317)\t11/23\t\tSFLD:SFLDG00002;SFLD:SFLDF00027;CDD:cd02608;Gene3D:1.20.1110.10;Pfam:PF13246;Gene3D:3.40.1110.10;TIGRFAM:TIGR01106;Gene3D:3.40.50.1000;Superfamily:SSF81665;Superfamily:SSF56784;Superfamily:SSF81660;PANTHER:PTHR43294:SF15;PANTHER:PTHR43294\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t2\t\t\t1\tCAGCTCGATGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nLIPE\t3991\tBI\tGRCh38\tchr19\t42410639\t42410639\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1087G>C\tp.Asp363His\tp.D363H\tENST00000244289\t2/10\t70\t56\t13\t32\t\t\tLIPE,missense_variant,p.D363H,ENST00000244289,NM_005357.4,c.1087G>C,MODERATE,YES,deleterious(0),possibly_damaging(0.88),-1;LIPE,missense_variant,p.D108H,ENST00000599783,,c.322G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;LIPE,missense_variant,p.D62H,ENST00000597001,,c.184G>C,MODERATE,,deleterious(0),possibly_damaging(0.88),-1;LIPE,missense_variant,p.D73H,ENST00000599211,,c.217G>C,MODERATE,,deleterious(0),probably_damaging(1),-1;LIPE,missense_variant,p.D62H,ENST00000601189,,c.184G>C,MODERATE,,deleterious(0),possibly_damaging(0.88),-1;LIPE,upstream_gene_variant,,ENST00000597620,,,MODIFIER,,,,-1;LIPE,upstream_gene_variant,,ENST00000599918,,,MODIFIER,,,,-1;LIPE,intron_variant,,ENST00000602000,,n.231-2317G>C,MODIFIER,,,,-1;LIPE,upstream_gene_variant,,ENST00000600224,,,MODIFIER,,,,-1;LIPE-AS1,intron_variant,,ENST00000594624,,n.51+13415C>G,MODIFIER,,,,1;LIPE-AS1,intron_variant,,ENST00000597203,,n.57+13415C>G,MODIFIER,,,,1;LIPE-AS1,downstream_gene_variant,,ENST00000593491,,,MODIFIER,,,,1;LIPE-AS1,downstream_gene_variant,,ENST00000599276,,,MODIFIER,,,,1\tG\tENSG00000079435\tENST00000244289\tTranscript\tmissense_variant\tmissense_variant\t1326/3768\t1087/3231\t363/1076\tD/H\tGac/Cac\tCOSV99734401\t\t-1\tLIPE\tHGNC\tHGNC:6621\tprotein_coding\tYES\tCCDS12607.1\tENSP00000244289\tQ05469.180\t\tUPI000013CB66\tQ05469-1\tNM_005357.4\tNM_005357.4\tP1\t\tdeleterious(0)\tpossibly_damaging(0.88)\t2/10\t\tPANTHER:PTHR23025;PANTHER:PTHR23025:SF1;Pfam:PF06350\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t1\tCAGGTCAAAGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPSG8\t440533\tBI\tGRCh38\tchr19\t42755144\t42755144\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.832C>G\tp.Gln278Glu\tp.Q278E\tENST00000306511\t4/5\t532\t494\t36\t458\t\t\tPSG8,missense_variant,p.Q278E,ENST00000404209,NM_001130167.2,c.832C>G,MODERATE,,tolerated(0.35),benign(0.007),-1;PSG8,missense_variant,p.Q185E,ENST00000401467,,c.553C>G,MODERATE,,deleterious(0.03),benign(0.16),-1;PSG8,missense_variant,p.Q156E,ENST00000406636,NM_001130168.2,c.466C>G,MODERATE,,deleterious(0.03),benign(0.012),-1;PSG8,missense_variant,p.Q278E,ENST00000306511,NM_182707.3,c.832C>G,MODERATE,YES,tolerated(0.36),benign(0.012),-1;PSG8,non_coding_transcript_exon_variant,,ENST00000469260,,n.862C>G,MODIFIER,,,,-1;PSG8,intron_variant,,ENST00000600709,,n.574-557C>G,MODIFIER,,,,-1;PSG8,3_prime_UTR_variant,,ENST00000478387,,c.*683C>G,MODIFIER,,,,-1;PSG8,non_coding_transcript_exon_variant,,ENST00000466163,,n.981C>G,MODIFIER,,,,-1\tC\tENSG00000124467\tENST00000306511\tTranscript\tmissense_variant\tmissense_variant\t929/1440\t832/1281\t278/426\tQ/E\tCag/Gag\tCOSV100126610;COSV60609151\t\t-1\tPSG8\tHGNC\tHGNC:9525\tprotein_coding\tYES\tCCDS33037.1\tENSP00000305005\tQ9UQ74.158\t\tUPI0000071471\tQ9UQ74-1\tNM_182707.3\tNM_182707.3\tA2\t\ttolerated(0.36)\tbenign(0.012)\t4/5\t\tPROSITE_profiles:PS50835;PANTHER:PTHR44427:SF3;PANTHER:PTHR44427;Gene3D:2.60.40.10;SMART:SM00409;SMART:SM00408;Superfamily:SSF48726\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1;1\t\tGCTCTGACCAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nIGFL4\t444882\tBI\tGRCh38\tchr19\t46040214\t46040214\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.273G>A\tp.Lys91=\tp.K91=\tENST00000377697\t3/4\t145\t114\t31\t82\t\t\tIGFL4,synonymous_variant,p.K91=,ENST00000377697,NM_001002923.2,c.273G>A,LOW,YES,,,-1;IGFL4,5_prime_UTR_variant,,ENST00000601672,,c.-10G>A,MODIFIER,,,,-1;IGFL4,downstream_gene_variant,,ENST00000595006,,,MODIFIER,,,,-1\tT\tENSG00000204869\tENST00000377697\tTranscript\tsynonymous_variant\tsynonymous_variant\t327/573\t273/375\t91/124\tK\taaG/aaA\tCOSV66619014\t\t-1\tIGFL4\tHGNC\tHGNC:32931\tprotein_coding\tYES\tCCDS33057.1\tENSP00000366926\tQ6B9Z1.94\t\tUPI00003FF1E1\t\tNM_001002923.2\t\tP1\t\t\t\t3/4\t\tPANTHER:PTHR34827;PANTHER:PTHR34827:SF1;Pfam:PF14653\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tGGGACCTTGAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM4539810\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNUCB1\t4924\tBI\tGRCh38\tchr19\t48919240\t48919240\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.956C>T\tp.Ala319Val\tp.A319V\tENST00000405315\t10/13\t76\t59\t17\t64\t\t\tNUCB1,missense_variant,p.A319V,ENST00000405315,NM_006184.6,c.956C>T,MODERATE,YES,tolerated(0.3),benign(0.197),1;NUCB1,missense_variant,p.A319V,ENST00000407032,,c.956C>T,MODERATE,,tolerated(0.3),benign(0.197),1;NUCB1,missense_variant,p.A289V,ENST00000424608,,c.866C>T,MODERATE,,tolerated(0.26),benign(0.015),1;NUCB1,downstream_gene_variant,,ENST00000452087,,,MODIFIER,,,,1;NUCB1,intron_variant,,ENST00000485798,,n.35-1914C>T,MODIFIER,,,,1;NUCB1,non_coding_transcript_exon_variant,,ENST00000492367,,n.241C>T,MODIFIER,,,,1;NUCB1,non_coding_transcript_exon_variant,,ENST00000465524,,n.582C>T,MODIFIER,,,,1;NUCB1,non_coding_transcript_exon_variant,,ENST00000469291,,n.425C>T,MODIFIER,,,,1;NUCB1,downstream_gene_variant,,ENST00000460125,,,MODIFIER,,,,1;NUCB1-AS1,upstream_gene_variant,,ENST00000416432,,,MODIFIER,YES,,,-1\tT\tENSG00000104805\tENST00000405315\tTranscript\tmissense_variant\tmissense_variant\t1028/2406\t956/1386\t319/461\tA/V\tgCa/gTa\tCOSV99618142\t\t1\tNUCB1\tHGNC\tHGNC:8043\tprotein_coding\tYES\tCCDS12740.1\tENSP00000385923\tQ02818.187\t\tUPI0000161F57\t\tNM_006184.6\tNM_006184.6\tP1\t\ttolerated(0.3)\tbenign(0.197)\t10/13\t\tPDB-ENSP_mappings:1snl.A;PROSITE_profiles:PS50222;PANTHER:PTHR19237:SF21;PANTHER:PTHR19237;Gene3D:1.10.238.10;Pfam:PF13499;Superfamily:SSF47473\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t6.763340024917852e-06\t0.0\t0.0\t0.0\t0.0\t0.00020226500055287033\t0.0\t0.0\t0.0\t0.0\t0.0\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCCTCGCATCCA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPTOV1\t53635\tBI\tGRCh38\tchr19\t49857055\t49857055\t+\tSilent\tSNP\tC\tC\tT\trs1046596920\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.639C>T\tp.Ile213=\tp.I213=\tENST00000391842\t6/12\t330\t294\t36\t332\t\t\tPTOV1,synonymous_variant,p.I213=,ENST00000391842,,c.639C>T,LOW,YES,,,1;PTOV1,synonymous_variant,p.I213=,ENST00000601675,NM_001364748.1&NM_017432.5,c.639C>T,LOW,,,,1;PTOV1,synonymous_variant,p.I213=,ENST00000599732,NM_001364750.1&NM_001305105.2,c.639C>T,LOW,,,,1;PTOV1,synonymous_variant,p.I181=,ENST00000600603,NM_001305108.1,c.543C>T,LOW,,,,1;PTOV1,synonymous_variant,p.I181=,ENST00000601638,NM_001364749.1&NM_001364747.1&NM_001364745.2,c.543C>T,LOW,,,,1;PTOV1,synonymous_variant,p.I228=,ENST00000594151,,c.684C>T,LOW,,,,1;PTOV1,synonymous_variant,p.I120=,ENST00000600793,,c.360C>T,LOW,,,,1;PNKP,downstream_gene_variant,,ENST00000322344,NM_007254.4,,MODIFIER,YES,,,-1;PNKP,downstream_gene_variant,,ENST00000596014,,,MODIFIER,,,,-1;PTOV1,upstream_gene_variant,,ENST00000597730,,,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000597965,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000600573,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000600910,,,MODIFIER,,,,-1;PTOV1,upstream_gene_variant,,ENST00000601093,,,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000631020,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000636840,,,MODIFIER,,,,-1;MIR4749,downstream_gene_variant,,ENST00000578197,,,MODIFIER,YES,,,1;PTOV1,non_coding_transcript_exon_variant,,ENST00000598325,,n.657C>T,MODIFIER,,,,1;PTOV1,non_coding_transcript_exon_variant,,ENST00000594165,,n.600C>T,MODIFIER,,,,1;PTOV1,non_coding_transcript_exon_variant,,ENST00000600105,,n.338C>T,MODIFIER,,,,1;PTOV1,downstream_gene_variant,,ENST00000594640,,,MODIFIER,,,,1;PTOV1,downstream_gene_variant,,ENST00000596095,,,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000596624,,,MODIFIER,,,,-1;PTOV1,synonymous_variant,p.I181=,ENST00000601612,,c.543C>T,LOW,,,,1;PTOV1,non_coding_transcript_exon_variant,,ENST00000595934,,n.552C>T,MODIFIER,,,,1;PTOV1,non_coding_transcript_exon_variant,,ENST00000597793,,n.920C>T,MODIFIER,,,,1;PTOV1,non_coding_transcript_exon_variant,,ENST00000596424,,n.13C>T,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000593706,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000593946,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000594661,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000595081,,,MODIFIER,,,,-1;PTOV1,downstream_gene_variant,,ENST00000598632,,,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000599454,,,MODIFIER,,,,-1;PTOV1,downstream_gene_variant,,ENST00000601501,,,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000601816,,,MODIFIER,,,,-1;PTOV1,downstream_gene_variant,,ENST00000602040,,,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000625216,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000627232,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000640501,,,MODIFIER,,,,-1;PTOV1-AS2,non_coding_transcript_exon_variant,,ENST00000593654,,n.511G>A,MODIFIER,,,,-1;PTOV1-AS2,downstream_gene_variant,,ENST00000599259,,,MODIFIER,,,,-1;AC018766.1,upstream_gene_variant,,ENST00000601211,,,MODIFIER,YES,,,-1;PTOV1-AS2,downstream_gene_variant,,ENST00000601893,,,MODIFIER,YES,,,-1\tT\tENSG00000104960\tENST00000391842\tTranscript\tsynonymous_variant\tsynonymous_variant\t809/1875\t639/1251\t213/416\tI\tatC/atT\trs1046596920;COSV55586361\t\t1\tPTOV1\tHGNC\tHGNC:9632\tprotein_coding\tYES\tCCDS12782.1\tENSP00000375717\tQ86YD1.134\t\tUPI000000DA02\tQ86YD1-1\t\t\tP1\t\t\t\t6/12\t\tPANTHER:PTHR12433;PANTHER:PTHR12433:SF3;Pfam:PF11232;Gene3D:2.40.290.30\t\t\t\t\t\t\t\t\t3.977e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.791e-06\t0.0\t0.0\t8.791e-06\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t\tSNV\t5\t\t0;1\t\tAAGATCTTCAT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPNKP\t11284\tBI\tGRCh38\tchr19\t49865142\t49865142\t+\tSilent\tSNP\tC\tC\tT\trs766200823\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.483G>A\tp.Val161=\tp.V161=\tENST00000322344\t4/17\t49\t34\t15\t53\t\t\tPNKP,synonymous_variant,p.V161=,ENST00000322344,NM_007254.4,c.483G>A,LOW,YES,,,-1;PNKP,synonymous_variant,p.V161=,ENST00000596014,,c.483G>A,LOW,,,,-1;PNKP,synonymous_variant,p.V161=,ENST00000600573,,c.483G>A,LOW,,,,-1;PNKP,synonymous_variant,p.V161=,ENST00000600910,,c.483G>A,LOW,,,,-1;PNKP,synonymous_variant,p.V161=,ENST00000631020,,c.483G>A,LOW,,,,-1;PNKP,synonymous_variant,p.V161=,ENST00000599543,,c.483G>A,LOW,,,,-1;PNKP,synonymous_variant,p.V81=,ENST00000627317,,c.243G>A,LOW,,,,-1;PNKP,synonymous_variant,p.V161=,ENST00000596726,,c.483G>A,LOW,,,,-1;AKT1S1,downstream_gene_variant,,ENST00000344175,NM_001098633.4,,MODIFIER,,,,-1;AKT1S1,downstream_gene_variant,,ENST00000391831,NM_001278159.1,,MODIFIER,,,,-1;AKT1S1,downstream_gene_variant,,ENST00000391832,NM_001098632.2,,MODIFIER,,,,-1;AKT1S1,downstream_gene_variant,,ENST00000391833,,,MODIFIER,,,,-1;AKT1S1,downstream_gene_variant,,ENST00000391834,NM_001278160.1,,MODIFIER,,,,-1;AKT1S1,downstream_gene_variant,,ENST00000391835,NM_032375.5,,MODIFIER,YES,,,-1;PTOV1,downstream_gene_variant,,ENST00000391842,,,MODIFIER,YES,,,1;PTOV1,downstream_gene_variant,,ENST00000597730,,,MODIFIER,,,,1;PNKP,upstream_gene_variant,,ENST00000597965,,,MODIFIER,,,,-1;PTOV1,downstream_gene_variant,,ENST00000599732,NM_001364750.1&NM_001305105.2,,MODIFIER,,,,1;PTOV1,downstream_gene_variant,,ENST00000600603,NM_001305108.1,,MODIFIER,,,,1;PTOV1,downstream_gene_variant,,ENST00000601093,,,MODIFIER,,,,1;PTOV1,downstream_gene_variant,,ENST00000601638,NM_001364749.1&NM_001364747.1&NM_001364745.2,,MODIFIER,,,,1;PTOV1,downstream_gene_variant,,ENST00000601675,NM_001364748.1&NM_017432.5,,MODIFIER,,,,1;PNKP,upstream_gene_variant,,ENST00000636840,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000636994,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000637897,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000638016,,,MODIFIER,,,,-1;PNKP,upstream_gene_variant,,ENST00000596624,,,MODIFIER,,,,-1;PTOV1,downstream_gene_variant,,ENST00000598325,,,MODIFIER,,,,1;PNKP,upstream_gene_variant,,ENST00000637325,,,MODIFIER,,,,-1;PNKP,synonymous_variant,p.V161=,ENST00000627232,,c.483G>A,LOW,,,,-1;PNKP,3_prime_UTR_variant,,ENST00000593946,,c.*410G>A,MODIFIER,,,,-1;PNKP,3_prime_UTR_variant,,ENST00000636214,,c.*20G>A,MODIFIER,,,,-1;PNKP,non_coding_transcript_exon_variant,,ENST00000594661,,n.897G>A,MODIFIER,,,,-1;PNKP,non_coding_transcript_exon_variant,,ENST00000625299,,n.401G>A,MODIFIER,,,,-1;PNKP,intron_variant,,ENST00000629179,,n.183-739G>A,MODIFIER,,,,-1;PNKP,upstream_gene_variant,,ENST00000593706,,,MODIFIER,,,,-1;PNKP,upstream_gene_variant,,ENST00000595081,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000595792,,,MODIFIER,,,,-1;PTOV1,downstream_gene_variant,,ENST00000597793,,,MODIFIER,,,,1;PNKP,downstream_gene_variant,,ENST00000598020,,,MODIFIER,,,,-1;PNKP,upstream_gene_variant,,ENST00000599454,,,MODIFIER,,,,-1;PTOV1,downstream_gene_variant,,ENST00000601612,,,MODIFIER,,,,1;PNKP,upstream_gene_variant,,ENST00000601816,,,MODIFIER,,,,-1;PNKP,upstream_gene_variant,,ENST00000625216,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000626274,,,MODIFIER,,,,-1;PNKP,downstream_gene_variant,,ENST00000629088,,,MODIFIER,,,,-1;PNKP,upstream_gene_variant,,ENST00000640501,,,MODIFIER,,,,-1\tT\tENSG00000039650\tENST00000322344\tTranscript\tsynonymous_variant\tsynonymous_variant\t604/1731\t483/1566\t161/521\tV\tgtG/gtA\trs766200823;COSV99681504\t\t-1\tPNKP\tHGNC\tHGNC:9154\tprotein_coding\tYES\tCCDS12783.1\tENSP00000323511\tQ96T60.180\t\tUPI00000705EA\tQ96T60-1\tNM_007254.4\tNM_007254.4\tP1\t\t\t\t4/17\t\tPANTHER:PTHR12083;TIGRFAM:TIGR01664;TIGRFAM:TIGR01663;Gene3D:3.40.50.1000;Superfamily:SSF56784\t\t\t\t\t\t\t\t\t4.008e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t3.267e-05\t3.267e-05\tgnomAD_SAS\t6.7570299506769516e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.542830068501644e-05\t0.0\t0.0\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t0;1\t1\tGGTTTCACCCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nKLK1\t3816\tBI\tGRCh38\tchr19\t50821848\t50821848\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs149251777\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.70C>T\tp.Arg24Trp\tp.R24W\tENST00000301420\t2/5\t47\t35\t12\t70\t\t\tKLK1,missense_variant,p.R24W,ENST00000301420,NM_002257.4,c.70C>T,MODERATE,YES,deleterious(0.03),probably_damaging(0.995),-1;KLK15,downstream_gene_variant,,ENST00000326856,NM_001277081.1,,MODIFIER,,,,-1;KLK15,downstream_gene_variant,,ENST00000596931,NM_001277082.1,,MODIFIER,,,,-1;KLK15,downstream_gene_variant,,ENST00000598239,NM_017509.3,,MODIFIER,YES,,,-1;LINC01869,downstream_gene_variant,,ENST00000326989,,,MODIFIER,,,,1;LINC01869,downstream_gene_variant,,ENST00000593632,,,MODIFIER,,,,1;LINC01869,downstream_gene_variant,,ENST00000634979,,,MODIFIER,,,,1;LINC01869,downstream_gene_variant,,ENST00000635639,,,MODIFIER,YES,,,1;KLK1,3_prime_UTR_variant,,ENST00000593325,,c.*879C>T,MODIFIER,,,,-1;KLK1,non_coding_transcript_exon_variant,,ENST00000593859,,n.109C>T,MODIFIER,,,,-1;KLK1,upstream_gene_variant,,ENST00000596300,,,MODIFIER,,,,-1;KLK15,downstream_gene_variant,,ENST00000596531,,,MODIFIER,,,,-1;KLK15,downstream_gene_variant,,ENST00000601680,,,MODIFIER,,,,-1;KLK15,downstream_gene_variant,,ENST00000602114,,,MODIFIER,,,,-1;LINC01869,downstream_gene_variant,,ENST00000651210,,,MODIFIER,,,,1\tA\tENSG00000167748\tENST00000301420\tTranscript\tmissense_variant\tmissense_variant\t109/876\t70/789\t24/262\tR/W\tCgg/Tgg\trs149251777\t\t-1\tKLK1\tHGNC\tHGNC:6357\tprotein_coding\tYES\tCCDS12804.1\tENSP00000301420\tP06870.202\tA0A1R3UCD2.24\tUPI000004CA0D\tP06870-1\tNM_002257.4\tNM_002257.4\tP1\t\tdeleterious(0.03)\tprobably_damaging(0.995)\t2/5\t\tPANTHER:PTHR24271;PANTHER:PTHR24271:SF47;SMART:SM00020\t\t\t\t\t\t\t0.0\t0.0001163\t2.404e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t5.32e-05\t0.0\t0.0\t0.0001163\tEA\t4.7323501348728314e-05\t2.4309600121341646e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t9.259829676011577e-05\t0.0\t0.0\t9.259829676011577e-05\tnfe\t\t\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t\t1\tAATCCGGGACT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF582\t147948\tBI\tGRCh38\tchr19\t56384663\t56384663\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.754G>A\tp.Glu252Lys\tp.E252K\tENST00000301310\t5/5\t30\t24\t6\t32\t\t\tZNF582,missense_variant,p.E252K,ENST00000301310,NM_144690.3,c.754G>A,MODERATE,YES,tolerated(0.07),probably_damaging(0.985),-1;ZNF582,missense_variant,p.E252K,ENST00000586929,NM_001320371.2,c.754G>A,MODERATE,,tolerated(0.07),probably_damaging(0.985),-1;ZNF582,intron_variant,,ENST00000589143,,c.232+5338G>A,MODIFIER,,,,-1;ZNF542P,downstream_gene_variant,,ENST00000495307,,,MODIFIER,,,,1;ZNF582,downstream_gene_variant,,ENST00000587778,,,MODIFIER,,,,-1;ZNF582,downstream_gene_variant,,ENST00000593145,,,MODIFIER,,,,-1;SLC25A36P1,upstream_gene_variant,,ENST00000590111,,,MODIFIER,YES,,,1;AC006116.4,upstream_gene_variant,,ENST00000589671,,,MODIFIER,YES,,,1;AC006116.9,downstream_gene_variant,,ENST00000651165,,,MODIFIER,YES,,,1\tT\tENSG00000018869\tENST00000301310\tTranscript\tmissense_variant\tmissense_variant\t913/2824\t754/1554\t252/517\tE/K\tGag/Aag\tCOSV100018951;COSV56732409\t\t-1\tZNF582\tHGNC\tHGNC:26421\tprotein_coding\tYES\tCCDS33121.1\tENSP00000301310\tQ96NG8.148\tA0A024R4P7.50\tUPI000006D278\t\tNM_144690.3\t\tP1\t\ttolerated(0.07)\tprobably_damaging(0.985)\t5/5\t\tGene3D:3.30.160.60;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF115;Superfamily:SSF57667\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1;1\t\tTTTCTCACCAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2\nZNF835\t90485\tBI\tGRCh38\tchr19\t56664740\t56664740\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.459G>A\tp.Leu153=\tp.L153=\tENST00000537055\t2/2\t100\t74\t25\t72\t\t\tZNF835,synonymous_variant,p.L153=,ENST00000537055,NM_001005850.3,c.459G>A,LOW,YES,,,-1;ZNF835,downstream_gene_variant,,ENST00000601659,,,MODIFIER,,,,-1;ZIM2-AS1,intron_variant,,ENST00000650950,,n.202-2537C>T,MODIFIER,YES,,,1\tT\tENSG00000127903\tENST00000537055\tTranscript\tsynonymous_variant\tsynonymous_variant\t688/3448\t459/1614\t153/537\tL\tctG/ctA\tCOSV101606403\t\t-1\tZNF835\tHGNC\tHGNC:34332\tprotein_coding\tYES\tCCDS56105.1\tENSP00000444747\tQ9Y2P0.153\t\tUPI0000EE7244\t\tNM_001005850.3\tNM_001005850.3\tP1\t\t\t\t2/2\t\tGene3D:3.30.160.60;Pfam:PF00096;PROSITE_patterns:PS00028;PROSITE_profiles:PS50157;PANTHER:PTHR24390;PANTHER:PTHR24390:SF73;SMART:SM00355;Superfamily:SSF57667;Superfamily:SSF57667\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t2\t\t1\t\tAGGGTCAGGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF749\t388567\tBI\tGRCh38\tchr19\t57443875\t57443875\t+\tNonsense_Mutation\tSNP\tC\tC\tT\trs562343206\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.727C>T\tp.Gln243Ter\tp.Q243*\tENST00000334181\t3/3\t123\t105\t18\t61\t\t\tZNF749,stop_gained,p.Q243*,ENST00000334181,NM_001321952.2&NM_001321953.2&NM_001023561.4,c.727C>T,HIGH,YES,,,1;AC004076.1,intron_variant,,ENST00000596831,,c.348-5783G>A,MODIFIER,YES,,,-1;ZNF749,downstream_gene_variant,,ENST00000415248,NM_001321954.2,,MODIFIER,,,,1\tT\tENSG00000186230\tENST00000334181\tTranscript\tstop_gained\tstop_gained\t981/4207\t727/2337\t243/778\tQ/*\tCag/Tag\trs562343206;COSV100494495\t\t1\tZNF749\tHGNC\tHGNC:32783\tprotein_coding\tYES\tCCDS33132.2\tENSP00000333980\tO43361.161\t\tUPI0000237933\t\tNM_001321952.2;NM_001321953.2;NM_001023561.4\tNM_001023561.4\tP1\t\t\t\t3/3\t\tGene3D:3.30.160.60;PROSITE_profiles:PS50157;PANTHER:PTHR24381;PANTHER:PTHR24381:SF5;Superfamily:SSF57667;Superfamily:SSF57667\t\t\t\t\t\t\t\t\t3.984e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.816e-06\t0.0\t0.0\t8.816e-06\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tHIGH\t1\tSNV\t2\t\t0;1\t\tAATATCAGCAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZIK1\t284307\tBI\tGRCh38\tchr19\t57590269\t57590269\t+\tMissense_Mutation\tSNP\tC\tC\tT\trs772757003\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.458C>T\tp.Ser153Leu\tp.S153L\tENST00000597850\t4/4\t100\t85\t14\t77\t\t\tZIK1,missense_variant,p.S153L,ENST00000597850,NM_001010879.4,c.458C>T,MODERATE,YES,tolerated(0.11),benign(0.006),1;ZIK1,missense_variant,p.S140L,ENST00000536878,NM_001321145.2&NM_001321147.2,c.419C>T,MODERATE,,tolerated(0.1),benign(0.046),1;ZIK1,missense_variant,p.S98L,ENST00000599456,NM_001321146.2,c.293C>T,MODERATE,,tolerated(0.08),benign(0.006),1;ZIK1,3_prime_UTR_variant,,ENST00000307468,,c.*202C>T,MODIFIER,,,,1;ZIK1,downstream_gene_variant,,ENST00000597219,,,MODIFIER,,,,1;ZIK1,downstream_gene_variant,,ENST00000598689,,,MODIFIER,,,,1;ZIK1,downstream_gene_variant,,ENST00000600053,,,MODIFIER,,,,1;ZIK1,downstream_gene_variant,,ENST00000598726,,,MODIFIER,,,,1\tT\tENSG00000171649\tENST00000597850\tTranscript\tmissense_variant\tmissense_variant\t670/4291\t458/1464\t153/487\tS/L\ttCa/tTa\trs772757003;COSV100277661\t\t1\tZIK1\tHGNC\tHGNC:33104\tprotein_coding\tYES\tCCDS33135.1\tENSP00000472867\tQ3SY52.129\t\tUPI00001609B2\tQ3SY52-1\tNM_001010879.4\tNM_001010879.4\tP4\t\ttolerated(0.11)\tbenign(0.006)\t4/4\t\tPANTHER:PTHR24377;PANTHER:PTHR24377:SF688\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t0;1\t\tAGCCTCATATG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nZNF8\t7554\tBI\tGRCh38\tchr19\t58295493\t58295493\t+\tMissense_Mutation\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1685C>T\tp.Ser562Phe\tp.S562F\tENST00000621650\t4/4\t117\t98\t19\t74\t\t\tZNF8,missense_variant,p.S562F,ENST00000621650,NM_021089.3,c.1685C>T,MODERATE,YES,tolerated(0.12),benign(0.022),1;AC020915.4,3_prime_UTR_variant,,ENST00000637233,,c.*1609C>T,MODIFIER,YES,,,1;ZNF8-ERVK3-1,non_coding_transcript_exon_variant,,ENST00000591325,,n.3263C>T,MODIFIER,YES,,,1\tT\tENSG00000278129\tENST00000621650\tTranscript\tmissense_variant\tmissense_variant\t1812/9110\t1685/1728\t562/575\tS/F\ttCt/tTt\tCOSV99544553\t\t1\tZNF8\tHGNC\tHGNC:13154\tprotein_coding\tYES\tCCDS12974.1\tENSP00000477716\tP17098.197\t\tUPI0000185FEA\t\tNM_021089.3\tNM_021089.3\tP1\t\ttolerated(0.12)\tbenign(0.022)\t4/4\t\tPANTHER:PTHR24377;PANTHER:PTHR24377:SF622\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tGCCTTCTGTGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nRASSF2\t9770\tBI\tGRCh38\tchr20\t4788269\t4788269\t+\tSplice_Site\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.640-1G>C\t\tp.X214_splice\tENST00000379376\t\t68\t55\t13\t63\t\t\tRASSF2,splice_acceptor_variant,p.X214_splice,ENST00000379376,NM_170774.1,c.640-1G>C,HIGH,,,,-1;RASSF2,splice_acceptor_variant,p.X214_splice,ENST00000379400,NM_014737.3,c.640-1G>C,HIGH,YES,,,-1;RASSF2,splice_acceptor_variant,,ENST00000478553,,n.663-1G>C,HIGH,,,,-1\tG\tENSG00000101265\tENST00000379376\tTranscript\tsplice_acceptor_variant\tsplice_acceptor_variant\t\t\t\t\t\tCOSV101040934\t\t-1\tRASSF2\tHGNC\tHGNC:9883\tprotein_coding\t\tCCDS13083.1\tENSP00000368684\tP50749.161\t\tUPI0000001C0A\tP50749-1\tNM_170774.1\t\tP1\t\t\t\t\t7/10\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tHIGH\t\tSNV\t1\t\t1\t\tTCAATCTGAAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\tNonExonic\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nFLRT3\t23767\tBI\tGRCh38\tchr20\t14327119\t14327119\t+\tSilent\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.388C>T\tp.Leu130=\tp.L130=\tENST00000341420\t3/3\t60\t41\t19\t75\t\t\tFLRT3,synonymous_variant,p.L130=,ENST00000341420,NM_198391.3,c.388C>T,LOW,YES,,,-1;FLRT3,synonymous_variant,p.L130=,ENST00000378053,NM_013281.3,c.388C>T,LOW,,,,-1;MACROD2,intron_variant,,ENST00000217246,NM_001351661.2&NM_001351663.2&NM_080676.6,c.272-166360G>A,MODIFIER,,,,1;MACROD2,intron_variant,,ENST00000642719,,c.272-166360G>A,MODIFIER,YES,,,1;MACROD2,intron_variant,,ENST00000477147,,n.541-166360G>A,MODIFIER,,,,1;MACROD2,intron_variant,,ENST00000490428,,n.263-166360G>A,MODIFIER,,,,1;MACROD2,intron_variant,,ENST00000494602,,n.299-166360G>A,MODIFIER,,,,1;FLRT3,downstream_gene_variant,,ENST00000462077,,,MODIFIER,,,,-1\tA\tENSG00000125848\tENST00000341420\tTranscript\tsynonymous_variant\tsynonymous_variant\t843/4977\t388/1950\t130/649\tL\tCtg/Ttg\tCOSV99443130\t\t-1\tFLRT3\tHGNC\tHGNC:3762\tprotein_coding\tYES\tCCDS13121.1\tENSP00000339912\tQ9NZU0.184\t\tUPI0000001BE7\t\tNM_198391.3\tNM_198391.3\tP1\t\t\t\t3/3\t\tGene3D:3.80.10.10;PDB-ENSP_mappings:5cmn.A;PDB-ENSP_mappings:5cmn.B;PDB-ENSP_mappings:5cmn.C;PDB-ENSP_mappings:5cmn.D;PDB-ENSP_mappings:5cmp.A;PDB-ENSP_mappings:5cmp.B;PDB-ENSP_mappings:5cmp.C;PDB-ENSP_mappings:5cmp.D;PDB-ENSP_mappings:6jbu.B;PROSITE_profiles:PS51450;PANTHER:PTHR45712;PANTHER:PTHR45712:SF12;SMART:SM00369;Superfamily:SSF52058\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t2\t\t1\t1\tTTCCAGATAGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nEDEM2\t55741\tBI\tGRCh38\tchr20\t35123909\t35123909\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1095G>C\tp.Glu365Asp\tp.E365D\tENST00000374492\t9/11\t66\t52\t14\t72\t\t\tEDEM2,missense_variant,p.E365D,ENST00000374492,NM_018217.3&NM_001355008.2,c.1095G>C,MODERATE,YES,tolerated(0.21),benign(0.21),-1;EDEM2,missense_variant,p.E328D,ENST00000374491,NM_001145025.2,c.984G>C,MODERATE,,tolerated(0.22),benign(0.134),-1\tG\tENSG00000088298\tENST00000374492\tTranscript\tmissense_variant\tmissense_variant\t1173/1884\t1095/1737\t365/578\tE/D\tgaG/gaC\tCOSV100993843\t\t-1\tEDEM2\tHGNC\tHGNC:15877\tprotein_coding\tYES\tCCDS13247.1\tENSP00000363616\tQ9BV94.172\t\tUPI00001285D9\tQ9BV94-1\tNM_018217.3;NM_001355008.2\tNM_018217.3\tP1\t\ttolerated(0.21)\tbenign(0.21)\t9/11\t\tPANTHER:PTHR45679;PANTHER:PTHR45679:SF6;Gene3D:1.50.10.10;Pfam:PF01532;Superfamily:SSF48225\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tTAGCCCTCTCG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nERGIC3\t51614\tBI\tGRCh38\tchr20\t35557011\t35557011\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.918G>C\tp.Glu306Asp\tp.E306D\tENST00000348547\t11/13\t42\t25\t17\t50\t\t\tERGIC3,missense_variant,p.E311D,ENST00000357394,NM_198398.2,c.933G>C,MODERATE,,tolerated(0.23),benign(0.257),1;ERGIC3,missense_variant,p.E306D,ENST00000348547,NM_015966.3,c.918G>C,MODERATE,,tolerated(0.23),possibly_damaging(0.524),1;ERGIC3,missense_variant,p.E320D,ENST00000416206,,c.960G>C,MODERATE,YES,tolerated(0.23),possibly_damaging(0.457),1;ERGIC3,missense_variant,p.E308D,ENST00000413587,,c.924G>C,MODERATE,,tolerated(0.26),benign(0.051),1;ERGIC3,missense_variant,p.E169D,ENST00000640748,,c.507G>C,MODERATE,,tolerated(0.22),benign(0.268),1;ERGIC3,missense_variant,p.E53D,ENST00000451605,,c.159G>C,MODERATE,,tolerated(0.23),benign(0.356),1;ERGIC3,missense_variant,p.E96D,ENST00000442139,,c.288G>C,MODERATE,,tolerated(0.26),possibly_damaging(0.669),1;ERGIC3,non_coding_transcript_exon_variant,,ENST00000488935,,n.209G>C,MODIFIER,,,,1;ERGIC3,downstream_gene_variant,,ENST00000482338,,,MODIFIER,,,,1;ERGIC3,non_coding_transcript_exon_variant,,ENST00000488384,,n.402G>C,MODIFIER,,,,1;ERGIC3,non_coding_transcript_exon_variant,,ENST00000465298,,n.420G>C,MODIFIER,,,,1;ERGIC3,downstream_gene_variant,,ENST00000475211,,,MODIFIER,,,,1;ERGIC3,downstream_gene_variant,,ENST00000496172,,,MODIFIER,,,,1;FER1L4,downstream_gene_variant,,ENST00000611673,,,MODIFIER,,,,-1;FER1L4,downstream_gene_variant,,ENST00000613061,,,MODIFIER,,,,-1;FER1L4,downstream_gene_variant,,ENST00000616283,,,MODIFIER,,,,-1;FER1L4,downstream_gene_variant,,ENST00000616711,,,MODIFIER,,,,-1;FER1L4,downstream_gene_variant,,ENST00000621044,,,MODIFIER,,,,-1;FER1L4,downstream_gene_variant,,ENST00000674470,,,MODIFIER,,,,-1;FER1L4,downstream_gene_variant,,ENST00000615531,,,MODIFIER,YES,,,-1\tC\tENSG00000125991\tENST00000348547\tTranscript\tmissense_variant\tmissense_variant\t938/1302\t918/1152\t306/383\tE/D\tgaG/gaC\tCOSV53413962;COSV99482019\t\t1\tERGIC3\tHGNC\tHGNC:15927\tprotein_coding\t\tCCDS13257.1\tENSP00000341358\tQ9Y282.146\tA2TJK5.92\tUPI000006DD39\tQ9Y282-1\tNM_015966.3\tNM_015966.3\tP4\t\ttolerated(0.23)\tpossibly_damaging(0.524)\t11/13\t\tPANTHER:PTHR10984:SF25;PANTHER:PTHR10984;Pfam:PF07970\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1;1\t\tCATGAGAAGGT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSGK2\t10110\tBI\tGRCh38\tchr20\t43579975\t43579975\t+\tMissense_Mutation\tSNP\tG\tG\tC\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1033G>C\tp.Glu345Gln\tp.E345Q\tENST00000341458\t11/12\t74\t52\t22\t75\t\t\tSGK2,missense_variant,p.E345Q,ENST00000341458,NM_016276.3,c.1033G>C,MODERATE,YES,deleterious(0.01),possibly_damaging(0.487),1;SGK2,missense_variant,p.E285Q,ENST00000423407,NM_001199264.1,c.853G>C,MODERATE,,deleterious(0.02),possibly_damaging(0.487),1;SGK2,missense_variant,p.E285Q,ENST00000373100,NM_170693.3,c.853G>C,MODERATE,,deleterious(0.02),possibly_damaging(0.487),1;SGK2,missense_variant,p.E311Q,ENST00000426287,,c.931G>C,MODERATE,,deleterious(0.02),benign(0.35),1;SGK2,downstream_gene_variant,,ENST00000648530,,,MODIFIER,,,,1;SGK2,stop_lost,p.*286Sext*2,ENST00000496343,,c.857G>C,HIGH,,,,1;SGK2,missense_variant,p.E285Q,ENST00000373077,,c.853G>C,MODERATE,,deleterious(0.01),probably_damaging(0.911),1;SGK2,non_coding_transcript_exon_variant,,ENST00000647716,,n.788G>C,MODIFIER,,,,1\tC\tENSG00000101049\tENST00000341458\tTranscript\tmissense_variant\tmissense_variant\t1252/2120\t1033/1284\t345/427\tE/Q\tGag/Cag\tCOSV100414845\t\t1\tSGK2\tHGNC\tHGNC:13900\tprotein_coding\tYES\tCCDS13320.1\tENSP00000340608\tQ9HBY8.171\t\tUPI0000033528\tQ9HBY8-1\tNM_016276.3\t\t\t\tdeleterious(0.01)\tpossibly_damaging(0.487)\t11/12\t\tPROSITE_profiles:PS50011;CDD:cd05603;PANTHER:PTHR24351:SF180;PANTHER:PTHR24351;Gene3D:1.10.510.10;Pfam:PF00069;Gene3D:3.30.200.20;SMART:SM00220;Superfamily:SSF56112\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tAGCTTGAGATT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCCN5\t8839\tBI\tGRCh38\tchr20\t44727099\t44727099\t+\tMissense_Mutation\tSNP\tC\tC\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.545C>A\tp.Ser182Tyr\tp.S182Y\tENST00000190983\t4/4\t147\t101\t46\t128\t\t\tCCN5,missense_variant,p.S182Y,ENST00000372868,NM_003881.3&NM_001323370.1,c.545C>A,MODERATE,YES,tolerated(0.12),benign(0.162),1;CCN5,missense_variant,p.L100M,ENST00000372865,NM_001323369.1,c.298C>A,MODERATE,,tolerated_low_confidence(0.16),possibly_damaging(0.458),1;CCN5,missense_variant,p.S182Y,ENST00000190983,,c.545C>A,MODERATE,,tolerated(0.12),benign(0.162),1;CCN5,non_coding_transcript_exon_variant,,ENST00000471629,,n.1349C>A,MODIFIER,,,,1;CCN5,non_coding_transcript_exon_variant,,ENST00000465000,,n.403C>A,MODIFIER,,,,1;KCNK15-AS1,intron_variant,,ENST00000427303,,n.233-10306G>T,MODIFIER,,,,-1;KCNK15-AS1,intron_variant,,ENST00000427598,,n.78-10306G>T,MODIFIER,YES,,,-1;KCNK15-AS1,intron_variant,,ENST00000445420,,n.146+11721G>T,MODIFIER,,,,-1\tA\tENSG00000064205\tENST00000190983\tTranscript\tmissense_variant\tmissense_variant\t691/1403\t545/753\t182/250\tS/Y\ttCt/tAt\tCOSV99509479\t\t1\tCCN5\tHGNC\tHGNC:12770\tprotein_coding\t\tCCDS13336.1\tENSP00000190983\tO76076.166\t\tUPI0000037219\tO76076-1\t\t\tP1\t\ttolerated(0.12)\tbenign(0.162)\t4/4\t\tPANTHER:PTHR11348;PANTHER:PTHR11348:SF22\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tGTTTTCTGGCC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nNPEPL1\t79716\tBI\tGRCh38\tchr20\t58694478\t58694478\t+\tSilent\tSNP\tC\tC\tT\trs760086884\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.393C>T\tp.Phe131=\tp.F131=\tENST00000356091\t3/12\t138\t96\t42\t139\t\t\tNPEPL1,synonymous_variant,p.F131=,ENST00000356091,NM_024663.4,c.393C>T,LOW,YES,,,1;NPEPL1,synonymous_variant,p.F103=,ENST00000525967,NM_001204872.2,c.309C>T,LOW,,,,1;NPEPL1,synonymous_variant,p.F83=,ENST00000525817,NM_001204873.2,c.249C>T,LOW,,,,1;NPEPL1,synonymous_variant,p.F20=,ENST00000533788,,c.60C>T,LOW,,,,1;STX16-NPEPL1,3_prime_UTR_variant,,ENST00000530122,,c.*376C>T,MODIFIER,YES,,,1;NPEPL1,non_coding_transcript_exon_variant,,ENST00000529976,,n.811C>T,MODIFIER,,,,1;NPEPL1,non_coding_transcript_exon_variant,,ENST00000527587,,n.801C>T,MODIFIER,,,,1;STX16-NPEPL1,downstream_gene_variant,,ENST00000413559,,,MODIFIER,,,,1\tT\tENSG00000215440\tENST00000356091\tTranscript\tsynonymous_variant\tsynonymous_variant\t494/2191\t393/1572\t131/523\tF\tttC/ttT\trs760086884;COSV100622589\t\t1\tNPEPL1\tHGNC\tHGNC:16244\tprotein_coding\tYES\tCCDS46621.1\tENSP00000348395\tQ8NDH3.152\t\tUPI000036789E\tQ8NDH3-1\tNM_024663.4\tNM_024663.4\tP1\t\t\t\t3/12\t\tGene3D:3.40.50.10590;Pfam:PF18295;PANTHER:PTHR11963;PANTHER:PTHR11963:SF4;CDD:cd00433\t\t\t\t\t\t\t\t\t2.008e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t4.433e-05\t0.0\t0.0\t4.433e-05\tgnomAD_NFE\t6.758310064469697e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t1.5430699932039715e-05\t0.0\t0.0\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t0;1\t\tGCCTTCCCGCT\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCECR2\t27443\tBI\tGRCh38\tchr22\t17537157\t17537157\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs868448604\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1223G>A\tp.Gly408Glu\tp.G408E\tENST00000342247\t11/20\t102\t71\t30\t91\t\t\tCECR2,missense_variant,p.G366E,ENST00000612582,,c.1097G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;CECR2,missense_variant,p.G408E,ENST00000342247,NM_001290047.2,c.1223G>A,MODERATE,YES,deleterious(0),probably_damaging(0.999),1;CECR2,missense_variant,p.G225E,ENST00000400585,NM_001290046.1,c.674G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;CECR2,missense_variant,p.G225E,ENST00000262608,,c.674G>A,MODERATE,,deleterious(0),probably_damaging(0.999),1;AC007666.2,intron_variant,,ENST00000651475,,n.334+5724C>T,MODIFIER,YES,,,-1\tA\tENSG00000099954\tENST00000342247\tTranscript\tmissense_variant\tmissense_variant\t1641/6178\t1223/4455\t408/1484\tG/E\tgGa/gAa\trs868448604;COSV99378335\t\t1\tCECR2\tHGNC\tHGNC:1840\tprotein_coding\tYES\t\tENSP00000341219\tQ9BXF3.160\t\tUPI0000DD0932\tQ9BXF3-1\tNM_001290047.2\t\tA2\t\tdeleterious(0)\tprobably_damaging(0.999)\t11/20\t\tPANTHER:PTHR47092\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t5\t\t0;1\t\tTCAAGGAAAGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nGNAZ\t2781\tBI\tGRCh38\tchr22\t23095720\t23095720\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.25G>A\tp.Glu9Lys\tp.E9K\tENST00000615612\t2/3\t72\t48\t24\t52\t\t\tGNAZ,missense_variant,p.E9K,ENST00000615612,NM_002073.4,c.25G>A,MODERATE,YES,deleterious(0.05),benign(0.029),1;RSPH14,intron_variant,,ENST00000216036,NM_014433.3,c.422-31587C>T,MODIFIER,YES,,,-1;GNAZ,downstream_gene_variant,,ENST00000492538,,,MODIFIER,,,,1\tA\tENSG00000128266\tENST00000615612\tTranscript\tmissense_variant\tmissense_variant\t526/3170\t25/1068\t9/355\tE/K\tGaa/Aaa\tCOSV50740741\t\t1\tGNAZ\tHGNC\tHGNC:4395\tprotein_coding\tYES\tCCDS13804.1\tENSP00000478892\tP19086.200\t\tUPI0000001249\t\tNM_002073.4\tNM_002073.4\tP1\t\tdeleterious(0.05)\tbenign(0.029)\t2/3\t\tLow_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;PANTHER:PTHR10218:SF65;PANTHER:PTHR10218\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t1\tSNV\t1\t\t1\t\tCAGAGGAAAAA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM3309365\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCABIN1\t23523\tBI\tGRCh38\tchr22\t24084783\t24084783\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.3115G>A\tp.Glu1039Lys\tp.E1039K\tENST00000263119\t21/37\t49\t37\t12\t41\t\t\tCABIN1,missense_variant,p.E1039K,ENST00000398319,NM_001199281.1,c.3115G>A,MODERATE,YES,tolerated(1),benign(0.001),1;CABIN1,missense_variant,p.E1039K,ENST00000263119,NM_012295.4,c.3115G>A,MODERATE,,tolerated(1),benign(0.001),1;CABIN1,missense_variant,p.E989K,ENST00000617531,NM_001201429.1,c.2965G>A,MODERATE,,tolerated(1),benign(0.026),1;CABIN1,missense_variant,p.E989K,ENST00000405822,,c.2965G>A,MODERATE,,tolerated(1),benign(0.003),1;CABIN1,upstream_gene_variant,,ENST00000496016,,,MODIFIER,,,,1\tA\tENSG00000099991\tENST00000263119\tTranscript\tmissense_variant\tmissense_variant;splice_region_variant\t3253/7233\t3115/6663\t1039/2220\tE/K\tGag/Aag\tCOSV99573296;COSV99574005\t\t1\tCABIN1\tHGNC\tHGNC:24187\tprotein_coding\t\tCCDS13823.1\tENSP00000263119\tQ9Y6J0.184\tA0A024R1E5.48\tUPI0000126D6C\tQ9Y6J0-1\tNM_012295.4\tNM_012295.4\tP4\t\ttolerated(1)\tbenign(0.001)\t21/37\t\tGene3D:1.25.40.10;PANTHER:PTHR15502;Superfamily:SSF48452\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1;1\t\tCAACTGAGGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nMYO18B\t84700\tBI\tGRCh38\tchr22\t25772361\t25772361\t+\tMissense_Mutation\tSNP\tG\tG\tA\trs751222865\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1720G>A\tp.Glu574Lys\tp.E574K\tENST00000536101\t7/43\t310\t235\t75\t210\t\t\tMYO18B,missense_variant,p.E574K,ENST00000335473,NM_032608.7,c.1720G>A,MODERATE,,deleterious(0),possibly_damaging(0.726),1;MYO18B,missense_variant,p.E574K,ENST00000407587,NM_001318245.2,c.1720G>A,MODERATE,YES,deleterious(0),possibly_damaging(0.656),1;MYO18B,missense_variant,p.E574K,ENST00000536101,,c.1720G>A,MODERATE,,deleterious(0),possibly_damaging(0.726),1;MYO18B,missense_variant,p.E574K,ENST00000539302,,c.1720G>A,MODERATE,,deleterious(0.01),possibly_damaging(0.794),1;MYO18B,non_coding_transcript_exon_variant,,ENST00000418374,,n.291G>A,MODIFIER,,,,1\tA\tENSG00000133454\tENST00000536101\tTranscript\tmissense_variant\tmissense_variant\t1979/8051\t1720/7704\t574/2567\tE/K\tGag/Aag\trs751222865;COSV59126310;COSV59129122\t\t1\tMYO18B\tHGNC\tHGNC:18150\tprotein_coding\t\tCCDS54507.1\tENSP00000441229\tQ8IUG5.160\t\tUPI0000207402\tQ8IUG5-1\t\t\tP4\t\tdeleterious(0)\tpossibly_damaging(0.726)\t7/43\t\tGene3D:3.40.850.10;Pfam:PF00063;PROSITE_profiles:PS51456;PANTHER:PTHR45615;PANTHER:PTHR45615:SF8;SMART:SM00242;Superfamily:SSF52540\t\t\t\t\t\t\t\t\t4.02e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t3.268e-05\t3.268e-05\tgnomAD_SAS\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t0;1;1\t1\tAGGTCGAGGAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\tCOSM4530707\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nCRYBB1\t1414\tBI\tGRCh38\tchr22\t26599574\t26599574\t+\tSilent\tSNP\tC\tC\tT\trs1393271770\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.675G>A\tp.Gln225=\tp.Q225=\tENST00000647684\t6/6\t108\t88\t20\t73\t\t\tCRYBB1,synonymous_variant,p.Q225=,ENST00000647684,NM_001887.4,c.675G>A,LOW,YES,,,-1;TPST2,upstream_gene_variant,,ENST00000403880,,,MODIFIER,,,,-1;CRYBB1,downstream_gene_variant,,ENST00000647569,,,MODIFIER,,,,-1;Z95115.2,intron_variant,,ENST00000668614,,n.56+2491C>T,MODIFIER,YES,,,1\tT\tENSG00000100122\tENST00000647684\tTranscript\tsynonymous_variant\tsynonymous_variant\t745/1041\t675/759\t225/252\tQ\tcaG/caA\trs1393271770;COSV99316204\t\t-1\tCRYBB1\tHGNC\tHGNC:2397\tprotein_coding\tYES\tCCDS13840.1\tENSP00000497249\tP53674.184\t\tUPI000000165D\t\tNM_001887.4\tNM_001887.4\tP1\t\t\t\t6/6\t\tGene3D:2.60.20.10;Pfam:PF00030;PROSITE_profiles:PS50915;PANTHER:PTHR11818;PANTHER:PTHR11818:SF12;SMART:SM00247;Superfamily:SSF49695\t\t\t\t\t\t\t\t\t3.984e-06\t0.0\t0.0\t0.0\t0.0\t0.0\t8.819e-06\t0.0\t0.0\t8.819e-06\tgnomAD_NFE\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t\t\t0;1\t1\tTGCATCTGTGG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nGAS2L1\t10634\tBI\tGRCh38\tchr22\t29312421\t29312421\t+\tMissense_Mutation\tSNP\tC\tC\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1970C>G\tp.Ser657Cys\tp.S657C\tENST00000616432\t6/6\t82\t65\t17\t54\t\t\tGAS2L1,missense_variant,p.S657C,ENST00000618518,,c.1970C>G,MODERATE,YES,tolerated_low_confidence(0.16),benign(0.322),1;GAS2L1,missense_variant,p.S657C,ENST00000616432,,c.1970C>G,MODERATE,,tolerated_low_confidence(0.16),benign(0.322),1;GAS2L1,missense_variant,p.S657C,ENST00000621062,NM_006478.5&NM_001362985.2,c.1970C>G,MODERATE,,tolerated_low_confidence(0.16),benign(0.322),1;GAS2L1,missense_variant,p.S657C,ENST00000611648,NM_152236.3,c.1970C>G,MODERATE,,tolerated_low_confidence(0.16),benign(0.322),1;GAS2L1,missense_variant,p.S430C,ENST00000406549,NM_001278730.2,c.1289C>G,MODERATE,,deleterious_low_confidence(0),benign(0.322),1;RASL10A,downstream_gene_variant,,ENST00000216101,NM_006477.5,,MODIFIER,YES,,,-1;RASL10A,downstream_gene_variant,,ENST00000401450,,,MODIFIER,,,,-1;GAS2L1,downstream_gene_variant,,ENST00000416823,,,MODIFIER,,,,1;GAS2L1,downstream_gene_variant,,ENST00000428622,,,MODIFIER,,,,1;GAS2L1,downstream_gene_variant,,ENST00000610653,,,MODIFIER,,,,1;RASL10A,downstream_gene_variant,,ENST00000474590,,,MODIFIER,,,,-1;RASL10A,downstream_gene_variant,,ENST00000608559,,,MODIFIER,,,,-1;GAS2L1,downstream_gene_variant,,ENST00000487341,,,MODIFIER,,,,1;GAS2L1,downstream_gene_variant,,ENST00000491016,,,MODIFIER,,,,1;AC002059.1,downstream_gene_variant,,ENST00000608014,,,MODIFIER,YES,,,-1\tG\tENSG00000185340\tENST00000616432\tTranscript\tmissense_variant\tmissense_variant\t2561/2925\t1970/2046\t657/681\tS/C\ttCc/tGc\tCOSV99329711\t\t1\tGAS2L1\tHGNC\tHGNC:16955\tprotein_coding\t\tCCDS74840.1\tENSP00000478908\t\tA0A5E8.112\tUPI0000073BD7\t\t\t\tP1\t\ttolerated_low_confidence(0.16)\tbenign(0.322)\t6/6\t\tPANTHER:PTHR46756;PANTHER:PTHR46756:SF16;MobiDB_lite:mobidb-lite;Low_complexity_(Seg):seg\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tCCCCTCCGGAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nGAL3ST1\t9514\tBI\tGRCh38\tchr22\t30555435\t30555435\t+\tMissense_Mutation\tSNP\tC\tC\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.790G>T\tp.Asp264Tyr\tp.D264Y\tENST00000338911\t2/2\t194\t157\t36\t185\t\t\tGAL3ST1,missense_variant,p.D264Y,ENST00000406361,NM_001318104.2&NM_001318108.2&NM_001318107.2,c.790G>T,MODERATE,YES,deleterious(0),probably_damaging(0.976),-1;GAL3ST1,missense_variant,p.D264Y,ENST00000402321,NM_001318106.2&NM_001318111.2,c.790G>T,MODERATE,,deleterious(0),probably_damaging(0.976),-1;GAL3ST1,missense_variant,p.D264Y,ENST00000401975,NM_001318110.2&NM_004861.3,c.790G>T,MODERATE,,deleterious(0),probably_damaging(0.976),-1;GAL3ST1,missense_variant,p.D264Y,ENST00000338911,NM_001318109.1&NM_001318105.2,c.790G>T,MODERATE,,deleterious(0),probably_damaging(0.976),-1;GAL3ST1,missense_variant,p.D264Y,ENST00000402369,NM_001318103.2,c.790G>T,MODERATE,,deleterious(0),probably_damaging(0.976),-1;GAL3ST1,missense_variant,p.D264Y,ENST00000406955,NM_001318112.2&NM_001318114.2&NM_001318113.2&NM_001318115.2&NM_001318116.2,c.790G>T,MODERATE,,deleterious(0),probably_damaging(0.976),-1;GAL3ST1,missense_variant,p.D264Y,ENST00000441967,,c.790G>T,MODERATE,,deleterious(0.01),probably_damaging(0.976),-1;GAL3ST1,missense_variant,p.D265Y,ENST00000431313,,c.793G>T,MODERATE,,deleterious(0),probably_damaging(0.978),-1;GAL3ST1,downstream_gene_variant,,ENST00000411821,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000416358,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000423299,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000423371,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000426220,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000427899,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000428682,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000437282,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000443136,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000445645,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000447224,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000448604,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000452827,,,MODIFIER,,,,-1;GAL3ST1,downstream_gene_variant,,ENST00000453479,,,MODIFIER,,,,-1\tA\tENSG00000128242\tENST00000338911\tTranscript\tmissense_variant\tmissense_variant\t984/1782\t790/1272\t264/423\tD/Y\tGac/Tac\tCOSV100143247;COSV58893872\t\t-1\tGAL3ST1\tHGNC\tHGNC:24240\tprotein_coding\t\tCCDS13879.1\tENSP00000343234\tQ99999.158\tA0A024R1D7.40\tUPI00001285C2\t\tNM_001318109.1;NM_001318105.2\t\tP1\t\tdeleterious(0)\tprobably_damaging(0.976)\t2/2\t\tPANTHER:PTHR14647;PANTHER:PTHR14647:SF56;Pfam:PF06990\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1;1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1;1\t\tCAGGTCCTTCA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nSMTN\t6525\tBI\tGRCh38\tchr22\t31088075\t31088075\t+\tSilent\tSNP\tC\tC\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.162C>T\tp.Phe54=\tp.F54=\tENST00000347557\t3/20\t64\t53\t11\t38\t\t\tSMTN,synonymous_variant,p.F110=,ENST00000612341,NM_001207018.1,c.330C>T,LOW,,,,1;SMTN,synonymous_variant,p.F54=,ENST00000333137,NM_001382639.1&NM_001382642.1&NM_001382645.1&NM_001382641.1&NM_001382647.1&NM_001382643.1&NM_001382638.1&NM_001382640.1&NM_001382644.1&NM_134269.3&NM_001382646.1,c.162C>T,LOW,,,,1;SMTN,synonymous_variant,p.F108=,ENST00000619644,NM_001207017.1,c.324C>T,LOW,YES,,,1;SMTN,synonymous_variant,p.F54=,ENST00000358743,NM_134270.3,c.162C>T,LOW,,,,1;SMTN,synonymous_variant,p.F54=,ENST00000347557,NM_006932.5,c.162C>T,LOW,,,,1;SMTN,synonymous_variant,p.F108=,ENST00000440425,,c.324C>T,LOW,,,,1;SMTN,synonymous_variant,p.F108=,ENST00000426927,,c.324C>T,LOW,,,,1;SMTN,synonymous_variant,p.F54=,ENST00000438223,,c.162C>T,LOW,,,,1;SMTN,synonymous_variant,p.F46=,ENST00000431481,,c.138C>T,LOW,,,,1;SMTN,5_prime_UTR_variant,,ENST00000416786,,c.-103C>T,MODIFIER,,,,1;SMTN,5_prime_UTR_variant,,ENST00000482444,,c.-162C>T,MODIFIER,,,,1;SMTN,downstream_gene_variant,,ENST00000422839,,,MODIFIER,,,,1;SMTN,downstream_gene_variant,,ENST00000432777,,,MODIFIER,,,,1;SMTN,upstream_gene_variant,,ENST00000455608,,,MODIFIER,,,,1;SMTN,non_coding_transcript_exon_variant,,ENST00000475548,,n.381C>T,MODIFIER,,,,1;SMTN,non_coding_transcript_exon_variant,,ENST00000489337,,n.379C>T,MODIFIER,,,,1;SMTN,non_coding_transcript_exon_variant,,ENST00000497697,,n.380C>T,MODIFIER,,,,1;SMTN,upstream_gene_variant,,ENST00000460658,,,MODIFIER,,,,1;SMTN,upstream_gene_variant,,ENST00000466272,,,MODIFIER,,,,1;AC005005.3,upstream_gene_variant,,ENST00000609017,,,MODIFIER,YES,,,-1\tT\tENSG00000183963\tENST00000347557\tTranscript\tsynonymous_variant\tsynonymous_variant\t380/3130\t162/2754\t54/917\tF\tttC/ttT\tCOSV100294908\t\t1\tSMTN\tHGNC\tHGNC:11126\tprotein_coding\t\tCCDS13886.1\tENSP00000328635\tP53814.180\t\tUPI000015FD9B\tP53814-1\tNM_006932.5\t\t\t\t\t\t3/20\t\tCoiled-coils_(Ncoils):Coil\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t\tSNV\t1\t\t1\t\tCGTTTCCGTGC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPOLR2F\t5435\tBI\tGRCh38\tchr22\t37956795\t37956795\t+\tMissense_Mutation\tSNP\tG\tG\tA\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.43G>A\tp.Asp15Asn\tp.D15N\tENST00000442738\t2/5\t81\t67\t14\t73\t\t\tPOLR2F,missense_variant,p.D15N,ENST00000442738,NM_021974.5,c.43G>A,MODERATE,,tolerated(0.11),probably_damaging(0.944),1;POLR2F,missense_variant,p.D15N,ENST00000606538,,c.43G>A,MODERATE,,deleterious(0.02),probably_damaging(0.944),1;POLR2F,missense_variant,p.D10N,ENST00000470701,,c.28G>A,MODERATE,,tolerated(0.14),probably_damaging(0.975),1;POLR2F,missense_variant,p.D15N,ENST00000407936,NM_001301130.2&NM_001301131.2,c.43G>A,MODERATE,YES,deleterious_low_confidence(0.03),probably_damaging(0.944),1;POLR2F,missense_variant,p.D15N,ENST00000488684,,c.43G>A,MODERATE,,tolerated_low_confidence(0.77),probably_damaging(0.99),1;POLR2F,missense_variant,p.D15N,ENST00000405557,,c.43G>A,MODERATE,,tolerated_low_confidence(0.09),probably_damaging(0.977),1;POLR2F,missense_variant,p.D15N,ENST00000460648,,c.43G>A,MODERATE,,tolerated(0.31),probably_damaging(0.99),1;POLR2F,5_prime_UTR_variant,,ENST00000492213,NM_001301129.2,c.-83G>A,MODIFIER,,,,1;C22orf23,upstream_gene_variant,,ENST00000249079,,,MODIFIER,,,,-1;C22orf23,upstream_gene_variant,,ENST00000403026,,,MODIFIER,,,,-1;C22orf23,upstream_gene_variant,,ENST00000403305,NM_032561.5,,MODIFIER,YES,,,-1;C22orf23,upstream_gene_variant,,ENST00000418863,,,MODIFIER,,,,-1;C22orf23,upstream_gene_variant,,ENST00000422191,,,MODIFIER,,,,-1;C22orf23,upstream_gene_variant,,ENST00000619227,NM_001207062.1,,MODIFIER,,,,-1;POLR2F,non_coding_transcript_exon_variant,,ENST00000484894,,n.232G>A,MODIFIER,,,,1;POLR2F,missense_variant,p.D15N,ENST00000443002,NM_001363825.1,c.43G>A,MODERATE,,tolerated(0.11),probably_damaging(0.99),1;POLR2F,missense_variant,p.D15N,ENST00000483713,,c.43G>A,MODERATE,,tolerated_low_confidence(0.77),probably_damaging(0.99),1\tA\tENSG00000100142\tENST00000442738\tTranscript\tmissense_variant\tmissense_variant\t132/2070\t43/384\t15/127\tD/N\tGat/Aat\tCOSV99970210\t\t1\tPOLR2F\tHGNC\tHGNC:9193\tprotein_coding\t\tCCDS13963.1\tENSP00000403852\tP61218.160\t\tUPI00001345E0\t\tNM_021974.5\tNM_021974.5\tP1\t\ttolerated(0.11)\tprobably_damaging(0.944)\t2/5\t\tPDB-ENSP_mappings:1qkl.A;PDB-ENSP_mappings:5iy6.F;PDB-ENSP_mappings:5iy7.F;PDB-ENSP_mappings:5iy8.F;PDB-ENSP_mappings:5iy9.F;PDB-ENSP_mappings:5iya.F;PDB-ENSP_mappings:5iyb.F;PDB-ENSP_mappings:5iyc.F;PDB-ENSP_mappings:5iyd.F;PDB-ENSP_mappings:6drd.F;PDB-ENSP_mappings:6o9l.F;Low_complexity_(Seg):seg;MobiDB_lite:mobidb-lite;MobiDB_lite:mobidb-lite;PANTHER:PTHR47227;PIRSF:PIRSF000778;PIRSF:PIRSF500154;Gene3D:3.90.940.10;Superfamily:SSF63562\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t6.758670224371599e-06\t2.4311999368364923e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t1\t\t1\t\tTTGATGATGTG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nPLXNB2\t23654\tBI\tGRCh38\tchr22\t50278997\t50278997\t+\tSilent\tSNP\tG\tG\tA\trs998895556\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.4404C>T\tp.Ile1468=\tp.I1468=\tENST00000359337\t28/37\t62\t40\t22\t55\t\t\tPLXNB2,synonymous_variant,p.I1468=,ENST00000359337,NM_001376869.1&NM_001376885.1&NM_001376866.1&NM_012401.4&NM_001376868.1&NM_001376886.1&NM_001376867.1&NM_001376879.1&NM_001376882.1&NM_001376873.1&NM_001376877.1&NM_001376883.1&NM_001376870.1&NM_001376864.1&NM_001376874.1&NM_001376872.1&NM_001376881.1,c.4404C>T,LOW,YES,,,-1;PLXNB2,synonymous_variant,p.I1468=,ENST00000449103,NM_001376865.1&NM_001376884.1&NM_001376878.1&NM_001376871.1&NM_001376876.1&NM_001376875.1&NM_001376880.1,c.4404C>T,LOW,,,,-1;PLXNB2,synonymous_variant,p.I100=,ENST00000614805,,c.300C>T,LOW,,,,-1;PLXNB2,5_prime_UTR_variant,,ENST00000610984,,c.-183C>T,MODIFIER,,,,-1;PLXNB2,intron_variant,,ENST00000411680,,c.203-301C>T,MODIFIER,,,,-1;PLXNB2,downstream_gene_variant,,ENST00000427829,,,MODIFIER,,,,-1;PLXNB2,downstream_gene_variant,,ENST00000496720,,,MODIFIER,,,,-1;PLXNB2,non_coding_transcript_exon_variant,,ENST00000479701,,n.1666C>T,MODIFIER,,,,-1;PLXNB2,non_coding_transcript_exon_variant,,ENST00000463165,,n.1206C>T,MODIFIER,,,,-1;PLXNB2,upstream_gene_variant,,ENST00000479818,,,MODIFIER,,,,-1;PLXNB2,downstream_gene_variant,,ENST00000492578,,,MODIFIER,,,,-1\tA\tENSG00000196576\tENST00000359337\tTranscript\tsynonymous_variant\tsynonymous_variant\t4571/6409\t4404/5517\t1468/1838\tI\tatC/atT\trs998895556;COSV100834299\t\t-1\tPLXNB2\tHGNC\tHGNC:9104\tprotein_coding\tYES\tCCDS43035.1\tENSP00000352288\tO15031.171\t\tUPI000003812D\t\tNM_001376869.1;NM_001376885.1;NM_001376866.1;NM_012401.4;NM_001376868.1;NM_001376886.1;NM_001376867.1;NM_001376879.1;NM_001376882.1;NM_001376873.1;NM_001376877.1;NM_001376883.1;NM_001376870.1;NM_001376864.1;NM_001376874.1;NM_001376872.1;NM_001376881.1\tNM_012401.4\tP1\t\t\t\t28/37\t\tPDB-ENSP_mappings:4e71.A;CDD:cd12792;PANTHER:PTHR22625;PANTHER:PTHR22625:SF9;Pfam:PF08337;Gene3D:1.10.506.10;Gene3D:3.10.20.90;Superfamily:SSF48350\t\t\t\t\t\t\t\t\t1.221e-05\t6.392e-05\t0.0\t0.0\t0.0001115\t0.0\t0.0\t0.0\t0.0\t0.0001115\tgnomAD_EAS\t6.759410098311491e-06\t2.4314300389960408e-05\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t0.0\t\t\t\t0;1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t5\t\t0;1\t\tTGCACGATCAC\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nAL133500.1\t0\tBI\tGRCh38\tchrX\t72301889\t72301889\t+\tMissense_Mutation\tSNP\tG\tG\tT\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.1592C>A\tp.Ser531Tyr\tp.S531Y\tENST00000648922\t12/12\t47\t22\t24\t35\t\t\tAL133500.1,missense_variant,p.S531Y,ENST00000648922,,c.1592C>A,MODERATE,YES,deleterious_low_confidence(0),unknown(0),-1;CITED1,missense_variant,p.S139Y,ENST00000246139,NM_004143.4,c.416C>A,MODERATE,,deleterious(0.01),benign(0.31),-1;CITED1,missense_variant,p.S165Y,ENST00000453707,,c.494C>A,MODERATE,YES,deleterious(0.01),benign(0.206),-1;CITED1,missense_variant,p.S165Y,ENST00000431381,NM_001144885.1,c.494C>A,MODERATE,,deleterious(0.01),benign(0.206),-1;CITED1,missense_variant,p.S139Y,ENST00000373619,NM_001144886.2,c.416C>A,MODERATE,,deleterious(0.01),benign(0.31),-1;CITED1,missense_variant,p.S139Y,ENST00000445983,,c.416C>A,MODERATE,,deleterious(0.01),benign(0.31),-1;CITED1,missense_variant,p.S139Y,ENST00000651998,NM_001144887.2,c.416C>A,MODERATE,,deleterious(0.01),benign(0.31),-1;CITED1,missense_variant,p.S139Y,ENST00000417400,,c.416C>A,MODERATE,,deleterious_low_confidence(0.01),benign(0.31),-1;CITED1,intron_variant,,ENST00000429794,,c.168-14C>A,MODIFIER,,,,-1;CITED1,downstream_gene_variant,,ENST00000427412,,,MODIFIER,,,,-1;CITED1,downstream_gene_variant,,ENST00000450875,,,MODIFIER,,,,-1;CITED1,downstream_gene_variant,,ENST00000454225,,,MODIFIER,,,,-1;AL133500.1,3_prime_UTR_variant,,ENST00000647613,,c.*1345C>A,MODIFIER,,,,-1;PIN4,intron_variant,,ENST00000439980,,c.*195+237G>T,MODIFIER,,,,1\tT\tENSG00000285547\tENST00000648922\tTranscript\tmissense_variant\tmissense_variant\t1674/1752\t1592/1670\t531/556\tS/Y\ttCt/tAt\tCOSV99860475\t\t-1\tAL133500.1\tClone_based_ensembl_gene\t\tprotein_coding\tYES\t\tENSP00000497072\t\tA0A3B3IRV1.7\tUPI000E6F3F9F\t\t\t\tP5\tcds_end_NF\tdeleterious_low_confidence(0)\tunknown(0)\t12/12\t\tPfam:PF04487\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tMODERATE\t\tSNV\t\t\t1\t\tCAGCAGAAGGA\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\nUTP14A\t10813\tBI\tGRCh38\tchrX\t129911087\t129911087\t+\tSilent\tSNP\tA\tA\tG\t\t\tTCGA-CV-A6JM-01A-11D-A31L-08\tTCGA-CV-A6JM-10A-01D-A31J-08\t\t\t\t\t\t\t\t\tSomatic\t\t\t\t\t\t\t7a8ba569-fd0e-4082-9584-45a4b35ce972\t1d09c286-6455-421e-8043-261a6060cb8d\tc.318A>G\tp.Gln106=\tp.Q106=\tENST00000394422\t5/15\t81\t31\t49\t56\t\t\tUTP14A,synonymous_variant,p.Q106=,ENST00000394422,NM_006649.4,c.318A>G,LOW,YES,,,1;UTP14A,synonymous_variant,p.Q106=,ENST00000425117,NM_001166221.1,c.318A>G,LOW,,,,1;UTP14A,upstream_gene_variant,,ENST00000427972,,,MODIFIER,,,,1;AL034405.1,intron_variant,,ENST00000432062,,n.207-2534T>C,MODIFIER,,,,-1;AL034405.1,intron_variant,,ENST00000660217,,n.239-2621T>C,MODIFIER,YES,,,-1;AL034405.1,intron_variant,,ENST00000670255,,n.197-2534T>C,MODIFIER,,,,-1\tG\tENSG00000156697\tENST00000394422\tTranscript\tsynonymous_variant\tsynonymous_variant\t365/2507\t318/2316\t106/771\tQ\tcaA/caG\tCOSV100929008\t\t1\tUTP14A\tHGNC\tHGNC:10665\tprotein_coding\tYES\tCCDS14615.1\tENSP00000377944\tQ9BVJ6.161\t\tUPI0000072A7B\tQ9BVJ6-1\tNM_006649.4\tNM_006649.4\tP1\t\t\t\t5/15\t\tPfam:PF04615;PANTHER:PTHR14150;PANTHER:PTHR14150:SF14\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t\t1\t\t\t\t\t\t\t\tLOW\t1\tSNV\t1\t\t1\t\tAAGCAACTGAG\t3b5ffb9f-1510-4608-b998-4a520f32ac74\te547d38f-e264-4c45-8051-48a5c815d14e\t08c95e8f-aa2f-4163-ac43-096053ec6886\t\t\tN\tUnknown\t\t\t\tmuse;mutect2;varscan2\n
## 1
## Frame_Shift_Del
## 2
## Frame_Shift_Ins
## 1
## Intron
## 2
## Missense_Mutation
## 81
## Nonsense_Mutation
## 5
## RNA
## 1
## Silent
## 52
## Splice_Region
## 1
## Splice_Site
## 2# Non silent mutations in genes
mut_data %>% filter(Variant_Classification != "Silent") %>% select(Hugo_Symbol)## Hugo_Symbol
## 1 CEP104
## 2 PUM1
## 3 HDAC1
## 4 MAGOH
## 5 NUP210L
## 6 GON4L
## 7 OR10K2
## 8 HSPA6
## 9 DDR2
## 10 CNTN2
## 11 MIA3
## 12 OBSCN
## 13 OR2M5
## 14 OR2M5
## 15 ASXL2
## 16 ABCG8
## 17 PAPOLG
## 18 M1AP
## 19 SEMA4F
## 20 NOSTRIN
## 21 SLC25A12
## 22 NEUROD1
## 23 ITGAV
## 24 CASP8
## 25 CRYGC
## 26 CUL3
## 27 DAW1
## 28 SPHKAP
## 29 ASB1
## 30 MYRIP
## 31 GXYLT2
## 32 SIDT1
## 33 CPA3
## 34 NLGN1
## 35 NAALADL2
## 36 PIK3CA
## 37 CCDC39
## 38 SORCS2
## 39 SLC4A4
## 40 MEPE
## 41 NEK1
## 42 TRIO
## 43 SLC38A9
## 44 PCDHAC1
## 45 KIF4B
## 46 KIF4B
## 47 MGAT4B
## 48 ZBED9
## 49 ITPR3
## 50 MAD2L1BP
## 51 LCA5
## 52 ZNF292
## 53 COQ3
## 54 FIG4
## 55 GRM1
## 56 ERMARD
## 57 SUGCT
## 58 CFTR
## 59 CASP2
## 60 KCTD9
## 61 CLVS1
## 62 FABP4
## 63 RIMS2
## 64 CSMD3
## 65 EXT1
## 66 ADCY8
## 67 GLI4
## 68 PLEC
## 69 CDKN2A
## 70 CREB3
## 71 C9orf40
## 72 TMEFF1
## 73 OR1L4
## 74 NOTCH1
## 75 ITGA8
## 76 ZNF32
## 77 AGAP7P
## 78 OGDHL
## 79 ANK3
## 80 EGR2
## 81 MYPN
## 82 CPEB3
## 83 TECTB
## 84 PNLIPRP3
## 85 PRLHR
## 86 CTBP2
## 87 BCCIP
## 88 DENND5A
## 89 ALX4
## 90 LRP4
## 91 TRIM48
## 92 SLC22A8
## 93 ATL3
## 94 STIP1
## 95 RASGRP2
## 96 AP000769.3# Mutation classes
table(mut_data %>% filter(Variant_Type=="SNP") %>%
mutate(nt_change = paste(Reference_Allele, Tumor_Seq_Allele2, sep = ">")) %>%
select(nt_change)
)## nt_change
## A>C A>G A>T C>A C>G C>T G>A G>C G>T T>A T>C
## 2 5 1 8 15 43 42 15 7 2 4